# HG changeset patch # User eschen42 # Date 1615495586 0 # Node ID 08d4ca8bc6dd7ce0b260bd78be095fd0da13f292 # Parent 1d36ecf93e674a2637c81de5f0fda6718a103328 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 9639dde5737c9aa2330bb603c2299345939407cf" diff -r 1d36ecf93e67 -r 08d4ca8bc6dd LICENSE --- a/LICENSE Thu Mar 11 20:44:23 2021 +0000 +++ b/LICENSE Thu Mar 11 20:46:26 2021 +0000 @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2017 Hegeman Lab +Copyright (c) 2017-2020 Adrian D. Hegeman's Laboratory Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff -r 1d36ecf93e67 -r 08d4ca8bc6dd README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Thu Mar 11 20:46:26 2021 +0000 @@ -0,0 +1,17 @@ +Galaxy Wrapper for the w4mclassfilter R Package +https://doi.org/10.5281/zenodo.1034793 + +This is a Galaxy tool-wrapper +https://docs.galaxyproject.org/en/latest/dev/schema.htm + +to wrap the w4mclassfilter R package +https://github.com/HegemanLab/w4mclassfilter + +for use with the Workflow4Metabolomics +https://workflow4metabolomics.org + +flavor of Galaxy +https://galaxyproject.org + +The tool is tested and deployed with Planemo +https://planemo.readthedocs.io/en/latest diff -r 1d36ecf93e67 -r 08d4ca8bc6dd README.md --- a/README.md Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,238 +0,0 @@ -[![DOI](https://zenodo.org/badge/90571457.svg)](https://zenodo.org/badge/latestdoi/90571457) Latest public release - -[![Build Status](https://travis-ci.org/HegemanLab/w4mclassfilter_galaxy_wrapper.svg?branch=master)](https://travis-ci.org/HegemanLab/w4mclassfilter_galaxy_wrapper) Current build status for master branch on GitHub - -[Repository 'w4mclassfilter' in Galaxy Toolshed](https://toolshed.g2.bx.psu.edu/repository?repository_id=5f24951d82ab40fa) - -# W4M Data Subset - -#### A Galaxy tool to select a subset of Workflow4Metabolomics data - -*W4M Data Subset* is [Galaxy tool-wrapper](https://docs.galaxyproject.org/en/latest/dev/schema.htm) to wrap the -[w4mclassfilter R package](https://github.com/HegemanLab/w4mclassfilter) for use with the -[Workflow4Metabolomics](http://workflow4metabolomics.org/) flavor of -[Galaxy](https://galaxyproject.org/). -This tool was developed and tested with [planemo](http://planemo.readthedocs.io/en/latest/). - -#### Author - -Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu) - -#### R package wrapped by this tool - -The *w4mclassfilter* package is available from the Hegeman lab github repository [https://github.com/HegemanLab/w4mclassfilter/releases](https://github.com/HegemanLab/w4mclassfilter/releases). - -#### Tool in Galaxy Toolshed - -The "w4mclassfilter" Galaxy tool, built from this repository, is in the main Galaxy Toolshed at [https://toolshed.g2.bx.psu.edu/repository?repository_id=5f24951d82ab40fa](https://toolshed.g2.bx.psu.edu/repository?repository_id=5f24951d82ab40fa) - -#### Tool updates - -See the **NEWS** section at the bottom of this page - -## Motivation - -LC-MS metabolomics experiments seek to resolve "features", i.e., species that have distinct chromatographic retention time ("rt") and (after ionization) mass-to-charge ratio ("*m/z*" or "mz"). -(If a chemical is fragmented or may have a variety of adducts, several features will result.) -Data for a sample are collected as mass-spectral intensities, each of -which is associated with a position on a 2D plane with dimensions of rt -and *m/z*. Ideally, features would be sufficiently reproducible among -sample-runs to distinguish features that are similar among samples from -those that differ. - -For liquid chromatography, the retention time for a species can vary considerably from one chromatography -run to the next. The Workflow4Metabolomics suite of Galaxy tools -(W4M, [Giacomoni *et al.*, 2014, Guitton *et al.* 2017]) -uses the XCMS preprocessing tools [Smith *et al.*, 2006] for "retention-time correction" to -align features among samples. Features may be better aligned if pooled -samples and blanks are included. - -Multivariate statistical tools may be used to discover clusters of -similar samples [Thévenot *et al.*, 2015]. -However, once retention-time alignment of features has been achieved -among samples in LC-MS datasets: - -- The presence of pools and blanks may confound identification and separation of sample clusters. -- Multivariate statistical algorithms may be impacted by missing values or dimensions that have zero variance. - - -## Description - -The W4M Data Subset tool selects subsets of samples, features, or data values and conditions the data for further analysis. - -- The tool takes as input the *dataMatrix*, *sampleMetadata*, and *variableMetadata* datasets produced by W4M\'s XCMS and CAMERA [Kuhl *et al.*, 2012] tools. -- The tool produces the same trio of output datasets, modified as described below. - -This tool can perform several operations to reduce the number samples or features to be analyzed (although *this should be done only in a statistically sound manner* consistent with the nature of the experiment): - -- *Sample filtering:* Samples may be selected by designating a "sample class" column in *sampleMetadata* and specifying criteria to include or exclude samples based on the contents of this column. -- *Feature filtering:* Features may be selected by specifying minimum or maximum value (or both) allowable in columns of *variableMetadata*. -- *Intensity filtering:* To exclude minimal features from consideration, a lower bound may be specified for the maximum intensity for a feature across all samples (i.e., for a row in *dataMatrix*). - -This tool also conditions data for statistical analysis: - -- Samples that are missing from either *sampleMetadata* or *dataMatrix* are eliminated. -- Features that are missing from either *variableMetadata* or *dataMatrix* are eliminated. -- Features and samples that have zero variance are eliminated. -- Samples and features are ordered consistently in *variableMetadata*, *sampleMetadata*, and *dataMatrix*. (The columns for sorting *variableMetadata* or *sampleMetadata* may be specified.) -- The names of the first columns of *variableMetadata* and *sampleMetadata* are set respectively to "variableMetadata" and "sampleMetadata". -- If desired, the values in the *dataMatrix* may be log-transformed. -- Negative intensities become missing values (before missing-value replacement is performed). -- If desired, each missing value in *dataMatrix* may be replaced with zero or the median value observed for the corresponding feature. -- If desired, a "center" for each treatment can be computed in lieu of the samples for that treatment. - -This tool may be applied several times sequentially, which may be useful for: - -- analyzing subsets of samples for progressively smaller sets of treatment levels, or -- choosing subsets of samples or features, respectively based on criteria in columns of *sampleMetadata* or *variableMetadata*. - -## NEWS - -### Changes in version 0.98.18 - -#### New features - -* Enhancement: Added option "compute center for each treatment" [https://github.com/HegemanLab/w4mclassfilter/issues/6](https://github.com/HegemanLab/w4mclassfilter/issues/6). -* Enhancement: Added option "enable sorting on multiple columns of metadata" [https://github.com/HegemanLab/w4mclassfilter/issues/7](https://github.com/HegemanLab/w4mclassfilter/issues/7). -* Enhancement: Added option "always treat negative intensities as missing values" [https://github.com/HegemanLab/w4mclassfilter\_galaxy\_wrapper/issues/7](https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/issues/7). - -#### Internal modifications - -* Use v0.98.18 of the [w4mclassfilter bioconda package](https://bioconda.github.io/recipes/w4mclassfilter/README.html). - - -### (Version numbers 0.98.15-0.98.17 skipped) - - -### Changes in version 0.98.14 - -#### New features - -* Enhancement [https://github.com/HegemanLab/w4mclassfilter\_galaxy\_wrapper/issues/6](https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/issues/6) - "Provide sort options for features and samples". - -#### Internal modifications - -* Use v0.98.14 of the [w4mclassfilter bioconda package](https://bioconda.github.io/recipes/w4mclassfilter/README.html). - -### Changes in version 0.98.13 - -#### New features - -* Support enhancement https://github.com/HegemanLab/w4mclassfilter/issues/4 - "add and test no-imputation and centering-imputation functions": - - Support no imputation. - - Support imputing missing feature-intensities as median intensity for the corresponding feature. - -#### Internal modifications - -* Use v0.98.13 of the [w4mclassfilter bioconda package](https://bioconda.github.io/recipes/w4mclassfilter/README.html). - - -### (Version number 0.98.12 skipped) - - -### Changes in version 0.98.11 - -#### New features - -* none - -#### Internal modifications - -* Use v0.98.8 of the [w4mclassfilter bioconda package](https://bioconda.github.io/recipes/w4mclassfilter/README.html). - -### Changes in version 0.98.10 - -#### New features - -* none - -#### Internal modifications - -* Quality-assurance improvements - Changes for IUC conformance and automated Planemo testing on Travis CI. -* Forbid hyphens in sample and variable names because R does not permit them. - -### Changes in version 0.98.9 - -#### New features - -* none - -#### Internal modifications - -* Added missing support for hyphen character in regular expressions - -### Changes in version 0.98.8 - -#### New features - -* The tool now appears in Galaxy with a new, more representative name: "W4M Data Subset". (Earlier versions of this tool appeared in Galaxy with the name "Sample Subset".) -* Option was added to log-transform data matrix values. -* Output datasets are named in conformance with the W4M convention of appending the name of each preprocessing tool to the input dataset name. -* Superfluous "Column that names the sample" input parameter was eliminated. -* Some documentation was updated or clarified. - -#### Internal modifications - -* None - -### Changes in version 0.98.7 - -#### New features - -* First column of output variableMetadata (that has feature names) now is always named "variableMetadata" -* First column of output sampleMetadata now (that has sample names) is always named "sampleMetadata" - -#### Internal modifications - -* Now uses w4mclassfilter R package v0.98.7. - -### Changes in version 0.98.6 - -#### New features - -* Added support for filtering out features whose attributes fall outside specified ranges. For more detail, see "Variable-range filters" above. - -#### Internal modifications - -* Now uses w4mclassfilter R package v0.98.6. -* Now sorts sample names and feature names in output files because some statistical tools expect the same order in dataMatrix row and column names as in the corresponding metadata files. - -### Changes in version 0.98.3 - -#### New features - -* Improved reference-list. - -#### Internal modifications - -* Improved input handling. -* Now uses w4mclassfilter R package v0.98.3, although that version has no functional implications for this tool. - -### Changes in version 0.98.1 - -#### New features - -* First release - Wrap the w4mclassfilter R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample. -* *dataMatrix* *is* modified by the tool, so it *does* appear as an output file -* *sampleMetadata* *is* modified by the tool, so it *does* appear as an output file -* *variableMetadata* *is* modified by the tool, so it *does* appear as an output file - -#### Internal modifications - -* none - -## Citations - -Benjamini, Yoav and Hochberg, Yosef (1995) **Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing.** In *Journal of the royal statistical society. Series B (Methodological), 1 (57), pp. pp. 289-300.* [http://www.jstor.org/stable/2346101](http://www.jstor.org/stable/2346101) - -Kuhl, Carsten and Tautenhahn, Ralf and Böttcher, Christoph and Larson, Tony R. and Neumann, Steffen (2011). **CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets.** In *Analytical Chemistry, 84 (1), pp. 283-289.* [doi:10.1021/ac202450g](http://dx.doi.org/10.1021/ac202450g) - -Giacomoni, F. and Le Corguille, G. and Monsoor, M. and Landi, M. and Pericard, P. and Petera, M. and Duperier, C. and Tremblay-Franco, M. and Martin, J.-F. and Jacob, D. and *et al.* (2014). **Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics.** In *Bioinformatics, 31 (9), pp. 1493–1495.* [doi:10.1093/bioinformatics/btu813](http://dx.doi.org/10.1093/bioinformatics/btu813) - -Guitton, Yann and Tremblay-Franco, Marie and Le Corguillé, Gildas and Martin, Jean-François and Pétéra, Mélanie and Roger-Mele, Pierrick and Delabrière, Alexis and Goulitquer, Sophie and Monsoor, Misharl and Duperier, Christophe and *et al.* (2017). **Create, run, share, publish, and reference your LC–MS, FIA–MS, GC–MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics.** In *The International Journal of Biochemistry & Cell Biology, pp. 89-101.* [doi:10.1016/j.biocel.2017.07.002](http://dx.doi.org/10.1016/j.biocel.2017.07.002) - -Smith, Colin A. and Want, Elizabeth J. and O'Maille, Grace and Abagyan, Ruben and Siuzdak, Gary (2006). **XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification.** In *Analytical Chemistry, 78 (3), pp. 779–787.* [doi:10.1021/ac051437y](http://dx.doi.org/10.1021/ac051437y) - -Thévenot, Etienne A. and Roux, Aurélie and Xu, Ying and Ezan, Eric and Junot, Christophe (2015). **Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses.** In *Journal of Proteome Research, 14 (8), pp. 3322–3335.* [doi:10.1021/acs.jproteome.5b00354](http://dx.doi.org/10.1021/acs.jproteome.5b00354) - -Yekutieli, Daniel and Benjamini, Yoav (2001) **The control of the false discovery rate in multiple testing under dependency.** In *The Annals of Statistics, 29 (4), pp. 1165-1188.* [doi:10.1214/aos/1013699998](http://dx.doi.org/10.1214/aos/1013699998) diff -r 1d36ecf93e67 -r 08d4ca8bc6dd docker_container_postbuild_setup_run.txt --- a/docker_container_postbuild_setup_run.txt Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -virtualenv .venv # initialize the virtual environment - do this once -. .venv/bin/activate # activate the virtual environment - do this each time you start using planemo -pip install planemo # install planemo into the virtual environment - do this once -# here is where I pull my project from github - depends on ~/.ssh -mkdir src -cd src -git clone git@github.com:HegemanLab/w4mclassfilter_galaxy_wrapper.git -cd w4mclassfilter_galaxy_wrapper/ -planemo conda_init . # initialize conda for planemo - do this once -planemo conda_install . # install the package dependencies using conda resolution - do this each time the dependencies change -./run_test.sh # wrapper that mainly does: planemo test --conda_dependency_resolution w4mclassfilter.xml -./run_serve.sh # wrapper that mainly does: planemo serve --host 0.0.0.0 --conda_dependency_resolution . -planemo shed_update -t testtoolshed . # deploy to testtoolshed - depends on ~/.planemo.yml diff -r 1d36ecf93e67 -r 08d4ca8bc6dd planemo_install_history.txt --- a/planemo_install_history.txt Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -#!/bin/bash - -# abridged transcript of the steps that I used to test this wrapper - -ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install)" - -sudo apt-get install build-essential - -cat >> ~/.bashrc << . -# ACE -export PATH="/home/backdoor/.linuxbrew/bin:$PATH" -export MANPATH="/home/backdoor/.linuxbrew/share/man:$MANPATH" -export INFOPATH="/home/backdoor/.linuxbrew/share/info:$INFOPATH" -. - -brew update -brew install python -brew tap galaxyproject/tap -brew install planemo - -git clone https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper.git -cd w4mclassfilter_galaxy_wrapper/ - -./run_test.sh diff -r 1d36ecf93e67 -r 08d4ca8bc6dd test-data/expected_dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected_dataMatrix.tsv Thu Mar 11 20:46:26 2021 +0000 @@ -0,0 +1,16 @@ + HU_017 HU_034 HU_078 HU_091 HU_093 HU_099 HU_130 HU_134 HU_138 +HMDB00191 560002 575790 785428 645785 591569 960658 639437 1092885 1409045 +HMDB00208 747080 595872 3143654 4059767 1433702 5593888 2477288 3346077 4230072 +HMDB00251 368600 94936 293988 352855 767894 268331 310918 1248919 577184 +HMDB00299 250551 456162 808657 614370 250403 768004 504108 1014041 1362408 +HMDB00512 525240 280560 556003 590779 209285 342532 569970 525240 246282 +HMDB00518 0 85944 129886 175800 13154 230242 440223 315368 10657 +HMDB00715 1252089 905408 5140022 2658555 814523 2558923 4184204 3865723 3236644 +HMDB01032 2569205 1604999 26222916 257139 675754 59906109 31151730 18648127 14989438 +HMDB01101 30689 52217 229568 4763576 3878773 976436 608298 1605075 72021 +HMDB01101.1 6877586 3158 4763576 3878773 976436 831937 1605075 72021 442510 +HMDB03193 76043 44943 173175 242549 57066 559869 339188 471368 262271 +HMDB04824 374028 539206 959381 605191 310260 1253319 477995 825691 1157093 +HMDB10348 47259 60885 168264 176500 76457 610110 279156 524468 451573 +HMDB13189 2644620 1661412 2755434 593863 837865 3526136 1608814 3446611 1941527 +HMDB59717 357351 301983 1028110 1530493 270027 1378535 808334 1132813 871209 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd test-data/expected_sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected_sampleMetadata.tsv Thu Mar 11 20:46:26 2021 +0000 @@ -0,0 +1,10 @@ +sampleMetadata injectionOrder mode age bmi gender +HU_017 2 pos 41 23.03 M +HU_034 9 pos 52 23.37 M +HU_078 34 pos 46 25.18 M +HU_091 42 pos 61 26.12 M +HU_093 43 pos 53 21.71 M +HU_099 46 pos 23 21.3 M +HU_130 63 pos 33 26.06 M +HU_134 67 pos 48 22.89 M +HU_138 68 pos 42 21.88 M diff -r 1d36ecf93e67 -r 08d4ca8bc6dd test-data/expected_variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected_variableMetadata.tsv Thu Mar 11 20:46:26 2021 +0000 @@ -0,0 +1,16 @@ +variableMetadata name mz rt +HMDB00191 loquor 650 600 +HMDB00208 loquimini 873 476 +HMDB00251 pasamur 500 423 +HMDB00299 bantur 700 500 +HMDB00512 pantur 900 543 +HMDB00518 loquoris 870 250 +HMDB00715 loquitur 725 900 +HMDB01032 loquimur 550 425 +HMDB01101 bar 150 300 +HMDB01101.1 baz 200 225 +HMDB03193 foo 100 200 +HMDB04824 loquantur 950 522 +HMDB10348 batur 300 275 +HMDB13189 baris 800 325 +HMDB59717 bamur 125 400 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd test-data/input_dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_dataMatrix.tsv Thu Mar 11 20:46:26 2021 +0000 @@ -0,0 +1,17 @@ +dataMatrix HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_204 HU_208 +HMDB03193 76043 412165 44943 27242 436566 173175 242549 57066 559869 3732 339188 471368 262271 127285 451270 212500 79673 NA 891129 43907 +HMDB01101 30689 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 891129 32742 +HMDB01101 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 72900 891129 30689 +HMDB10348 47259 544877 60885 34582 529874 168264 176500 76457 610110 16262 279156 524468 451573 591487 433529 161069 214392 13781 891129 39315 +HMDB59717 357351 1030464 301983 67604 306862 1028110 1530493 270027 1378535 289677 808334 1132813 871209 895435 715190 1563158 784738 146195 891129 239030 +HMDB00822 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 +HMDB13189 2644620 727587 1661412 619181 136278 2755434 593863 837865 3526136 2003278 1608814 3446611 1941527 113937 3132404 2893445 2092753 1034666 891129 841661 +HMDB00299 250551 1046138 456162 159386 1013302 808657 614370 250403 768004 242085 504108 1014041 1362408 1057660 1110050 566050 411886 142233 891129 284775 +HMDB00191 560002 771533 575790 392284 888498 785428 645785 591569 960658 910201 639437 1092885 1409045 2292023 1246459 1945577 710519 773384 891129 622898 +HMDB00518 -34236 58249 85944 NA 342102 129886 175800 13154 230242 NA 440223 315368 10657 419508 48673 28361 514579 23108 891129 73831 +HMDB00715 1252089 2547452 905408 371059 4983588 5140022 2658555 814523 2558923 859466 4184204 3865723 3236644 2615560 3820724 3577833 2295288 625924 891129 1341900 +HMDB01032 2569205 26023086 1604999 430453 8103558 26222916 257139 675754 59906109 263055 31151730 18648127 14989438 1554658 20249262 5588731 871010 15920 891129 44276 +HMDB00208 747080 13420742 595872 1172376 7172632 3143654 4059767 1433702 5593888 5402629 2477288 3346077 4230072 7621236 8960828 10335722 7037373 1574738 891129 2540044 +HMDB04824 374028 1144386 539206 178517 1046190 959381 605191 310260 1253319 477259 477995 825691 1157093 1089284 1411802 1020206 782673 346761 891129 387811 +HMDB00512 NA 319783 280560 85009 1333877 556003 590779 209285 342532 198512 569970 525240 246282 1140422 542345 1171008 827723 222953 891129 85554 +HMDB00251 368600 616555 94936 622468 180988 293988 352855 767894 268331 167246 310918 1248919 577184 10985 335711 403815 80614 63393 891129 616061 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd test-data/input_nofilter_dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_nofilter_dataMatrix.tsv Thu Mar 11 20:46:26 2021 +0000 @@ -0,0 +1,16 @@ +dataMatrix HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_204 HU_208 +HMDB03193 76043 412165 44943 27242 436566 173175 242549 57066 559869 3732 339188 471368 262271 127285 451270 212500 79673 NA 891129 43907 +HMDB01101 30689 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 891129 32742 +HMDB01101 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 72900 891129 30689 +HMDB10348 47259 544877 60885 34582 529874 168264 176500 76457 610110 16262 279156 524468 451573 591487 433529 161069 214392 13781 891129 39315 +HMDB59717 357351 1030464 301983 67604 306862 1028110 1530493 270027 1378535 289677 808334 1132813 871209 895435 715190 1563158 784738 146195 891129 239030 +HMDB00822 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 +HMDB00299 250551 1046138 456162 159386 1013302 808657 614370 250403 768004 242085 504108 1014041 1362408 1057660 1110050 566050 411886 142233 891129 284775 +HMDB00191 560002 771533 575790 392284 888498 785428 645785 591569 960658 910201 639437 1092885 1409045 2292023 1246459 1945577 710519 773384 891129 622898 +HMDB00518 -34236 58249 85944 NA 342102 129886 175800 13154 230242 NA 440223 315368 10657 419508 48673 28361 514579 23108 891129 73831 +HMDB00715 1252089 2547452 905408 371059 4983588 5140022 2658555 814523 2558923 859466 4184204 3865723 3236644 2615560 3820724 3577833 2295288 625924 891129 1341900 +HMDB01032 2569205 26023086 1604999 430453 8103558 26222916 257139 675754 59906109 263055 31151730 18648127 14989438 1554658 20249262 5588731 871010 15920 891129 44276 +HMDB00208 747080 13420742 595872 1172376 7172632 3143654 4059767 1433702 5593888 5402629 2477288 3346077 4230072 7621236 8960828 10335722 7037373 1574738 891129 2540044 +HMDB04824 374028 1144386 539206 178517 1046190 959381 605191 310260 1253319 477259 477995 825691 1157093 1089284 1411802 1020206 782673 346761 891129 387811 +HMDB00512 NA 319783 280560 85009 1333877 556003 590779 209285 342532 198512 569970 525240 246282 1140422 542345 1171008 827723 222953 891129 85554 +HMDB00251 368600 616555 94936 622468 180988 293988 352855 767894 268331 167246 310918 1248919 577184 10985 335711 403815 80614 63393 891129 616061 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd test-data/input_sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_sampleMetadata.tsv Thu Mar 11 20:46:26 2021 +0000 @@ -0,0 +1,21 @@ +sampleMetadata injectionOrder mode age bmi gender +HU_017 2 pos 41 23.03 M +HU_028 7 pos 41 23.92 F +HU_034 9 pos 52 23.37 M +HU_051 20 pos 24 23.23 F +HU_060 24 pos 55 28.72 F +HU_078 34 pos 46 25.18 M +HU_091 42 pos 61 26.12 M +HU_093 43 pos 53 21.71 M +HU_099 46 pos 23 21.3 M +HU_110 53 pos 50 20.9 F +HU_130 63 pos 33 26.06 M +HU_134 67 pos 48 22.89 M +HU_138 68 pos 42 21.88 M +HU_149 72 pos 35 19.49 F +HU_152 75 pos 26 17.58 F +HU_175 87 pos 35 21.26 F +HU_178 88 pos 60 32.87 F +HU_185 95 pos 42 21.09 F +HU_204 104 pos 31 29.06 M +HU_208 106 pos 27 18.61 F diff -r 1d36ecf93e67 -r 08d4ca8bc6dd test-data/input_variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_variableMetadata.tsv Thu Mar 11 20:46:26 2021 +0000 @@ -0,0 +1,17 @@ +variable name mz rt +HMDB03193 foo 100 200 +HMDB01101 bar 150 300 +HMDB01101 baz 200 225 +HMDB00208 loquimini 873 476 +HMDB10348 batur 300 275 +HMDB00299 bantur 700 500 +HMDB00191 loquor 650 600 +HMDB00518 loquoris 870 250 +HMDB59717 bamur 125 400 +HMDB00822 bamini 300 199 +HMDB13189 baris 800 325 +HMDB00715 loquitur 725 900 +HMDB01032 loquimur 550 425 +HMDB04824 loquantur 950 522 +HMDB00512 pantur 900 543 +HMDB00251 pasamur 500 423 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd test-data/rangefilter_dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rangefilter_dataMatrix.tsv Thu Mar 11 20:46:26 2021 +0000 @@ -0,0 +1,6 @@ + HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_149 HU_152 HU_175 HU_178 HU_185 HU_208 +HMDB00191 19.0950724540801 19.5573683394871 19.1351832076319 18.581538968171 19.7610090032025 19.5831195045026 19.3006944055142 19.1741869272827 19.8736633887651 19.7958256457729 19.2864427002132 21.1281900906526 20.2494039981067 20.8917666482316 19.438513703552 19.5608253922588 19.2486364146654 +HMDB00208 19.5109032146715 23.6779611010349 19.1846429313023 20.1610039089984 22.7740711828923 21.5840110083096 21.9529654992985 20.451313755289 22.4154199380002 22.3652301844309 21.2403301698498 22.8615935600174 23.0952006159265 23.3011358356974 22.746605551146 20.5866803867983 21.2764220576728 +HMDB01032 21.2928905785523 24.6332887213057 20.6141409677961 18.7154961966847 22.9501240553341 24.6443247870262 17.9721889132336 19.3661386209868 25.8361997953493 18.0050049466979 24.8928089492302 20.5681658146509 24.2713659930314 22.4140893053724 19.7323297568288 13.958552715431 15.4342372710269 +HMDB01101.1 22.7134708439962 15.6722319530667 11.6247954558602 23.3631578345615 17.8085620299575 22.183613575742 21.8871689158671 19.8971659609365 19.6661147561338 19.214418735272 20.6142092807528 20.079142288524 20.4818181509538 14.9315685693242 21.3775881248719 16.1536311941017 14.9054340159519 +HMDB13189 21.3346290086766 19.4727602406215 20.6639784491577 19.2400016764968 17.0561931543153 21.3938481405109 19.1797706242895 19.6763582845664 21.7496566885488 20.9339312108399 20.6175661105571 16.7978767996065 21.5788388647145 21.4643567902489 20.9969706149343 19.9807336965562 19.6828797432404 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd test-data/rangefilter_sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rangefilter_sampleMetadata.tsv Thu Mar 11 20:46:26 2021 +0000 @@ -0,0 +1,18 @@ +sampleMetadata injectionOrder mode age bmi gender +HU_017 2 pos 41 23.03 M +HU_028 7 pos 41 23.92 F +HU_034 9 pos 52 23.37 M +HU_051 20 pos 24 23.23 F +HU_060 24 pos 55 28.72 F +HU_078 34 pos 46 25.18 M +HU_091 42 pos 61 26.12 M +HU_093 43 pos 53 21.71 M +HU_099 46 pos 23 21.3 M +HU_110 53 pos 50 20.9 F +HU_130 63 pos 33 26.06 M +HU_149 72 pos 35 19.49 F +HU_152 75 pos 26 17.58 F +HU_175 87 pos 35 21.26 F +HU_178 88 pos 60 32.87 F +HU_185 95 pos 42 21.09 F +HU_208 106 pos 27 18.61 F diff -r 1d36ecf93e67 -r 08d4ca8bc6dd test-data/rangefilter_variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rangefilter_variableMetadata.tsv Thu Mar 11 20:46:26 2021 +0000 @@ -0,0 +1,6 @@ +variableMetadata name mz rt +HMDB00191 loquor 650 600 +HMDB00208 loquimini 873 476 +HMDB01032 loquimur 550 425 +HMDB01101.1 baz 200 225 +HMDB13189 baris 800 325 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd test_repositories.list --- a/test_repositories.list Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -tools/w4mclassfilter diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/old_w4mclassfilter.xml --- a/tools/old_w4mclassfilter.xml Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1146 +0,0 @@ - - Filter W4M data by values or metadata - - r-base - r-batch - w4mclassfilter - - &2); - [ ! 1 ]; - else - Rscript - $__tool_directory__/w4mclassfilter_wrapper.R - dataMatrix_in '$dataMatrix_in' - sampleMetadata_in '$sampleMetadata_in' - variableMetadata_in '$variableMetadata_in' - sampleclassNames '$sampleclassNames' - inclusive '$inclusive' - wildcards '$wildcards' - classnameColumn '$classnameColumn' - samplenameColumn 'sampleMetadata' - variable_range_filter '$variableRangeFilter' - transformation '$transformation' - imputation '$imputation' - dataMatrix_out '$dataMatrix_out' - sampleMetadata_out '$sampleMetadata_out' - variableMetadata_out '$variableMetadata_out' - order_vrbl '$order_vrbl' - order_smpl '$order_smpl' - centering '$centering'; - fi - ]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - é - - - 10.1093/bioinformatics/btu813 - - 10.1016/j.biocel.2017.07.002 - - 10.1021/ac202450g - - 10.1021/ac051437y - - 10.1021/acs.jproteome.5b00354 - - diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/LICENSE --- a/tools/w4mclassfilter/LICENSE Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2017-2020 Adrian D. Hegeman's Laboratory - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/README --- a/tools/w4mclassfilter/README Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -Galaxy Wrapper for the w4mclassfilter R Package -https://doi.org/10.5281/zenodo.1034793 - -This is a Galaxy tool-wrapper -https://docs.galaxyproject.org/en/latest/dev/schema.htm - -to wrap the w4mclassfilter R package -https://github.com/HegemanLab/w4mclassfilter - -for use with the Workflow4Metabolomics -https://workflow4metabolomics.org - -flavor of Galaxy -https://galaxyproject.org - -The tool is tested and deployed with Planemo -https://planemo.readthedocs.io/en/latest diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/quick_test.sh --- a/tools/w4mclassfilter/quick_test.sh Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#!/bin/bash - -# purge old output files -if [ -f test_log.txt ]; then rm test_log.txt; fi -if [ -f tool_test_output.html ]; then rm tool_test_output.html; fi -if [ -f tool_test_output.json ]; then rm tool_test_output.json; fi - -# run test and write new output files, showing progress to command line output -# planemo conda_install . -planemo test --conda_dependency_resolution w4mclassfilter.xml 2>&1 | grep -v -i observer | tee test_log.txt - -# summarize warnings and errors to command line output -grep -E "(ERROR)|(WARNING)" test_log.txt | grep -v samtools | grep -v "Dynamic Display Application links" | grep -v "twobit.loc" diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/run_serve.sh --- a/tools/w4mclassfilter/run_serve.sh Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -#!/bin/bash - -# run test and write new output files, showing progress to command line output -planemo conda_install . - -#planemo serve --host 0.0.0.0 --port 8389 --galaxy_root ~/planemo-dev/galaxy-dev . -planemo serve --host 0.0.0.0 . - diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/run_test.sh --- a/tools/w4mclassfilter/run_test.sh Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#!/bin/bash - -# purge old output files -if [ -f test_log.txt ]; then rm test_log.txt; fi -if [ -f tool_test_output.html ]; then rm tool_test_output.html; fi -if [ -f tool_test_output.json ]; then rm tool_test_output.json; fi - -# run test and write new output files, showing progress to command line output -planemo conda_install . -planemo test --conda_dependency_resolution w4mclassfilter.xml 2>&1 | grep -v -i observer | tee test_log.txt - -# summarize warnings and errors to command line output -grep -E "(ERROR)|(WARNING)" test_log.txt | grep -v samtools | grep -v "Dynamic Display Application links" | grep -v "twobit.loc" diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/exp_med1_medoid_dm.tsv --- a/tools/w4mclassfilter/test-data/exp_med1_medoid_dm.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ - X1 X8 X10 X26 X27 X28 X29 X35 X37 X44 X45 X50 X80 X85 X89 X134 X160 X183 X231 X345 X353 -trtA_1 0 0.00180737321564983 0 0 0 0 0 0 0 0 0.09826970333995 0.502704391270598 0 0 0 0.103676462792297 0 0 0.219609447733449 0 0.0303803032193031 -trtA_2 0 0 0.1499611203546 0 0.171306020866901 0.7407933477417 0 0.0317311746973008 1.0677832262992 0.4890197262973 0 0.251352195635299 0 0.0285671029685997 0.04320144565955 0 0.0256247716491007 0.243708505613103 0 0.0398841868243505 0.00253982134690034 -trtA_3 0 0.0300457862235994 0.0424174908139001 0 0.342612041733801 0 0.528508602842599 0.1222967572165 0.0147975909652498 3.869505334958 0.849339292282099 0 0.1934182113026 0.6387333497781 0.0864028913191 0.0518382313961485 0.411653240176999 0.121854252806552 0.439218895466897 0.183561229851001 0 -trtB_1 0 0 0 0 1.5113745967984 0 0 0 0.0295951819304996 0 0.1965394066799 0.251352195635299 0 0 0 0 0.0256247716491007 0 0.219609447733449 0.2933301023069 0.00507964269380068 -trtB_2 0 0.220593700553497 0.124637442941602 1.086467693902 0 0 0 0.0634623493946016 0 0.978039452594601 0 0.580225894218799 0 0.0571342059371993 0.357735292121102 0.140388243320103 0.0815161028168028 0.414790130357598 0.761398854361399 0.0398841868243505 0 -trtB_3 0 0.00180737321564983 0.0424174908139001 0 0.171306020866901 0 0 0.0317311746973008 0.0147975909652498 0.4890197262973 0.09826970333995 0 0 0.0285671029685997 0.04320144565955 0.0518382313961485 0 0.121854252806552 0 0 0.00253982134690034 -trtC_1 0 0 0 0 1.8589982127458 0.268514070203597 0.0667424385274984 1.9883459973714 0.269349110340201 1.2385296023128 1.1443146127588 0.754715219586299 0.752261526391599 0.125735401747001 0.7011594009854 0.0518382313961485 0.0512495432982014 0.320143072543999 0.679179854411199 0 0.730941378584301 -trtC_2 1.900985710853 0.00180737321564983 0.0848349816278002 0 0 0 0 0 0 0.4890197262973 0 0.251352195635299 0 0.0285671029685997 0 0.244624610443701 0.0256247716491007 0.121854252806552 0 0.0797683736487009 0 -trtC_3 0 0.00361474643129966 0.0424174908139001 0 0.171306020866901 0 0 0.0317311746973008 0.0147975909652498 0 0.09826970333995 0 0 0 0.04320144565955 0 0 0 0.219609447733449 0.0398841868243505 0.00253982134690034 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/exp_med1_medoid_sm.tsv --- a/tools/w4mclassfilter/test-data/exp_med1_medoid_sm.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -sampleMetadata medoid pcgroup mz rt -X1 M75T431 1 75.0246219750883 431.003601360729 -X8 M73T1061 8 72.9367161649113 1060.80034606296 -X10 M70T1043 10 70.0122929793033 1042.83709612962 -X26 M75T505 26 74.5552304268754 505.059650753422 -X27 M71T369 27 71.0488456490549 368.759546615083 -X28 M74T876_2 28 73.7524067558588 876.27549665073 -X29 M74T871 29 73.7524028205993 871.313876430572 -X35 M71T377 35 71.0488173286188 376.931518857336 -X37 M71T555 37 71.0489644640144 555.004553220191 -X44 M71T581 44 71.0490430805114 581.198136872667 -X45 M71T364 45 71.0488487473802 364.081506343325 -X50 M77T537 50 76.9819350151329 536.652145428441 -X80 M74T858 80 73.7524235616046 858.00252803859 -X85 M73T32_1 85 72.9368652358215 31.7025769021219 -X89 M71T1041 89 70.9909558511769 1041.40508992281 -X134 M71T138 134 70.7378907468715 137.798948287145 -X160 M73T1096 160 72.936874804031 1095.52504027727 -X183 M70T61 183 70.0651210994061 61.3905354181062 -X231 M74T1033 231 74.0963050198453 1033.01869720333 -X345 M74T33 345 73.5315669737491 33.3902011282139 -X353 M72T54 353 72.0807228513553 54.4048259006589 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/exp_med1_medoid_vm.tsv --- a/tools/w4mclassfilter/test-data/exp_med1_medoid_vm.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -variableMetadata sample trt -trtA_1 trtA_1 A -trtA_2 trtA_2 A -trtA_3 trtA_3 A -trtB_1 trtB_1 B -trtB_2 trtB_2 B -trtB_3 trtB_3 B -trtC_1 trtC_1 C -trtC_2 trtC_2 C -trtC_3 trtC_3 C diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/expected_dataMatrix.tsv --- a/tools/w4mclassfilter/test-data/expected_dataMatrix.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ - HU_017 HU_034 HU_078 HU_091 HU_093 HU_099 HU_130 HU_134 HU_138 -HMDB00191 560002 575790 785428 645785 591569 960658 639437 1092885 1409045 -HMDB00208 747080 595872 3143654 4059767 1433702 5593888 2477288 3346077 4230072 -HMDB00251 368600 94936 293988 352855 767894 268331 310918 1248919 577184 -HMDB00299 250551 456162 808657 614370 250403 768004 504108 1014041 1362408 -HMDB00512 525240 280560 556003 590779 209285 342532 569970 525240 246282 -HMDB00518 0 85944 129886 175800 13154 230242 440223 315368 10657 -HMDB00715 1252089 905408 5140022 2658555 814523 2558923 4184204 3865723 3236644 -HMDB01032 2569205 1604999 26222916 257139 675754 59906109 31151730 18648127 14989438 -HMDB01101 30689 52217 229568 4763576 3878773 976436 608298 1605075 72021 -HMDB01101.1 6877586 3158 4763576 3878773 976436 831937 1605075 72021 442510 -HMDB03193 76043 44943 173175 242549 57066 559869 339188 471368 262271 -HMDB04824 374028 539206 959381 605191 310260 1253319 477995 825691 1157093 -HMDB10348 47259 60885 168264 176500 76457 610110 279156 524468 451573 -HMDB13189 2644620 1661412 2755434 593863 837865 3526136 1608814 3446611 1941527 -HMDB59717 357351 301983 1028110 1530493 270027 1378535 808334 1132813 871209 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/expected_sampleMetadata.tsv --- a/tools/w4mclassfilter/test-data/expected_sampleMetadata.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -sampleMetadata injectionOrder mode age bmi gender -HU_017 2 pos 41 23.03 M -HU_034 9 pos 52 23.37 M -HU_078 34 pos 46 25.18 M -HU_091 42 pos 61 26.12 M -HU_093 43 pos 53 21.71 M -HU_099 46 pos 23 21.3 M -HU_130 63 pos 33 26.06 M -HU_134 67 pos 48 22.89 M -HU_138 68 pos 42 21.88 M diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/expected_variableMetadata.tsv --- a/tools/w4mclassfilter/test-data/expected_variableMetadata.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -variableMetadata name mz rt -HMDB00191 loquor 650 600 -HMDB00208 loquimini 873 476 -HMDB00251 pasamur 500 423 -HMDB00299 bantur 700 500 -HMDB00512 pantur 900 543 -HMDB00518 loquoris 870 250 -HMDB00715 loquitur 725 900 -HMDB01032 loquimur 550 425 -HMDB01101 bar 150 300 -HMDB01101.1 baz 200 225 -HMDB03193 foo 100 200 -HMDB04824 loquantur 950 522 -HMDB10348 batur 300 275 -HMDB13189 baris 800 325 -HMDB59717 bamur 125 400 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/input_dataMatrix.tsv --- a/tools/w4mclassfilter/test-data/input_dataMatrix.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -dataMatrix HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_204 HU_208 -HMDB03193 76043 412165 44943 27242 436566 173175 242549 57066 559869 3732 339188 471368 262271 127285 451270 212500 79673 NA 891129 43907 -HMDB01101 30689 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 891129 32742 -HMDB01101 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 72900 891129 30689 -HMDB10348 47259 544877 60885 34582 529874 168264 176500 76457 610110 16262 279156 524468 451573 591487 433529 161069 214392 13781 891129 39315 -HMDB59717 357351 1030464 301983 67604 306862 1028110 1530493 270027 1378535 289677 808334 1132813 871209 895435 715190 1563158 784738 146195 891129 239030 -HMDB00822 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 -HMDB13189 2644620 727587 1661412 619181 136278 2755434 593863 837865 3526136 2003278 1608814 3446611 1941527 113937 3132404 2893445 2092753 1034666 891129 841661 -HMDB00299 250551 1046138 456162 159386 1013302 808657 614370 250403 768004 242085 504108 1014041 1362408 1057660 1110050 566050 411886 142233 891129 284775 -HMDB00191 560002 771533 575790 392284 888498 785428 645785 591569 960658 910201 639437 1092885 1409045 2292023 1246459 1945577 710519 773384 891129 622898 -HMDB00518 -34236 58249 85944 NA 342102 129886 175800 13154 230242 NA 440223 315368 10657 419508 48673 28361 514579 23108 891129 73831 -HMDB00715 1252089 2547452 905408 371059 4983588 5140022 2658555 814523 2558923 859466 4184204 3865723 3236644 2615560 3820724 3577833 2295288 625924 891129 1341900 -HMDB01032 2569205 26023086 1604999 430453 8103558 26222916 257139 675754 59906109 263055 31151730 18648127 14989438 1554658 20249262 5588731 871010 15920 891129 44276 -HMDB00208 747080 13420742 595872 1172376 7172632 3143654 4059767 1433702 5593888 5402629 2477288 3346077 4230072 7621236 8960828 10335722 7037373 1574738 891129 2540044 -HMDB04824 374028 1144386 539206 178517 1046190 959381 605191 310260 1253319 477259 477995 825691 1157093 1089284 1411802 1020206 782673 346761 891129 387811 -HMDB00512 NA 319783 280560 85009 1333877 556003 590779 209285 342532 198512 569970 525240 246282 1140422 542345 1171008 827723 222953 891129 85554 -HMDB00251 368600 616555 94936 622468 180988 293988 352855 767894 268331 167246 310918 1248919 577184 10985 335711 403815 80614 63393 891129 616061 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/input_med1_dm.tsv --- a/tools/w4mclassfilter/test-data/input_med1_dm.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -X M70T1043 M70T61 M71T138 M71T1041 M71T377 M71T369 M71T364 M71T555 M71T581 M72T34_1 M72T54 M72T34_3 M73T1061 M73T1044 M73T32_1 M73T1096 M73T32_2 M73T1043 M74T1042_1 M74T33 M74T871 M74T876_2 M74T858 M74T34 M74T1033 M75T34 M75T505 M75T431 M76T1040 M77T537 -trtA_1 0 0 0.103676462792297 0 0 0 0.09826970333995 0 0 0 0.0303803032193031 0 0.00180737321564983 0.174619941309 0 0 0 0 0 0 0 0 0 0 0.219609447733449 0 0 0 0.0151151439275008 0.502704391270598 -trtA_2 0.1499611203546 0.243708505613103 0 0.04320144565955 0.0317311746973008 0.171306020866901 0 1.0677832262992 0.4890197262973 0.140208039060401 0.00253982134690034 0.0563798353136988 0 0.00346576229545015 0.0285671029685997 0.0256247716491007 0.818318427514498 0.2150061358386 0.1234949545399 0.0398841868243505 0 0.7407933477417 0 0.0476545410972502 0 0.112811564993098 0 0 0 0.251352195635299 -trtA_3 0.0424174908139001 0.121854252806552 0.0518382313961485 0.0864028913191 0.1222967572165 0.342612041733801 0.849339292282099 0.0147975909652498 3.869505334958 0.285443289823299 0 0.112759670627398 0.0300457862235994 0 0.6387333497781 0.411653240176999 0.0933267742982 0.0514902142761002 0.0463451483315485 0.183561229851001 0.528508602842599 0 0.1934182113026 0.420661197739499 0.439218895466897 0.0175408561815491 0 0 0.1265423906184 0 -trtB_1 0 0 0 0 0 1.5113745967984 0.1965394066799 0.0295951819304996 0 0.280416078120801 0.00507964269380068 0 0 0.00346576229545015 0 0.0256247716491007 0.0933267742982 0 0.0463451483315485 0.2933301023069 0 0 0 0.935782704287199 0.219609447733449 0.0175408561815491 0 0 0.0151151439275008 0.251352195635299 -trtB_2 0.124637442941602 0.414790130357598 0.140388243320103 0.357735292121102 0.0634623493946016 0 0 0 0.978039452594601 0.140208039060401 0 0.0563798353136988 0.220593700553497 0.0767204072380991 0.0571342059371993 0.0815161028168028 0.446741706469403 0.0514902142761002 0 0.0398841868243505 0 0 0 0.0476545410972502 0.761398854361399 0 1.086467693902 0 0 0.580225894218799 -trtB_3 0.0424174908139001 0.121854252806552 0.0518382313961485 0.04320144565955 0.0317311746973008 0.171306020866901 0.09826970333995 0.0147975909652498 0.4890197262973 0 0.00253982134690034 0.2357122484906 0.00180737321564983 0 0.0285671029685997 0 0 0.1029804285522 0.204744259308601 0 0 0 0 0 0 0.0422615246151992 0 0 0.2218306650343 0 -trtC_1 0 0.320143072543999 0.0518382313961485 0.7011594009854 1.9883459973714 1.8589982127458 1.1443146127588 0.269349110340201 1.2385296023128 0 0.730941378584301 0.640778164724498 0 0.0069315245909003 0.125735401747001 0.0512495432982014 0 0 0 0 0.0667424385274984 0.268514070203597 0.752261526391599 0 0.679179854411199 0.0175408561815491 0 0 0.0302302878550016 0.754715219586299 -trtC_2 0.0848349816278002 0.121854252806552 0.244624610443701 0 0 0 0 0 0.4890197262973 0.513858474098299 0 0.0563798353136988 0.00180737321564983 0.00346576229545015 0.0285671029685997 0.0256247716491007 0.1866535485964 0.3576876580278 0.0926902966630969 0.0797683736487009 0 0 0 0.0953090821945004 0 0.0350817123630982 0 1.900985710853 0.0151151439275008 0.251352195635299 -trtC_3 0.0424174908139001 0 0 0.04320144565955 0.0317311746973008 0.171306020866901 0.09826970333995 0.0147975909652498 0 0.140208039060401 0.00253982134690034 0 0.00361474643129966 0 0 0 0.0933267742982 0.0514902142761002 0.0463451483315485 0.0398841868243505 0 0 0 0.0476545410972502 0.219609447733449 0 0 0 0 0 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/input_med1_sm.tsv --- a/tools/w4mclassfilter/test-data/input_med1_sm.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ -sampleMetadata pcgroup mz rt -M70T1043 10 70.0122929793033 1042.83709612962 -M70T61 183 70.0651210994061 61.3905354181062 -M71T138 134 70.7378907468715 137.798948287145 -M71T1041 89 70.9909558511769 1041.40508992281 -M71T377 35 71.0488173286188 376.931518857336 -M71T369 27 71.0488456490549 368.759546615083 -M71T364 45 71.0488487473802 364.081506343325 -M71T555 37 71.0489644640144 555.004553220191 -M71T581 44 71.0490430805114 581.198136872667 -M72T34_1 345 71.529455784918 33.7387759459325 -M72T54 353 72.0807228513553 54.4048259006589 -M72T34_3 345 72.0807426611777 33.8672738618788 -M73T1061 8 72.9367161649113 1060.80034606296 -M73T1044 10 72.9367229345106 1043.98726790638 -M73T32_1 85 72.9368652358215 31.7025769021219 -M73T1096 160 72.936874804031 1095.52504027727 -M73T32_2 85 73.0647299005977 32.166230277174 -M73T1043 10 73.1056566280053 1042.8817438948 -M74T1042_1 10 73.531470577532 1042.13833094273 -M74T33 345 73.5315669737491 33.3902011282139 -M74T871 29 73.7524028205993 871.313876430572 -M74T876_2 28 73.7524067558588 876.27549665073 -M74T858 80 73.7524235616046 858.00252803859 -M74T34 345 74.0319853847452 33.6736778224506 -M74T1033 231 74.0963050198453 1033.01869720333 -M75T34 345 74.5303776078914 33.8541677395798 -M75T505 26 74.5552304268754 505.059650753422 -M75T431 1 75.0246219750883 431.003601360729 -M76T1040 89 76.0391694122706 1039.93848585356 -M77T537 50 76.9819350151329 536.652145428441 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/input_med1_vm.tsv --- a/tools/w4mclassfilter/test-data/input_med1_vm.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -variableMetadata sample trt -trtA_1 trtA_1 A -trtA_2 trtA_2 A -trtA_3 trtA_3 A -trtB_1 trtB_1 B -trtB_2 trtB_2 B -trtB_3 trtB_3 B -trtC_1 trtC_1 C -trtC_2 trtC_2 C -trtC_3 trtC_3 C diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/input_nofilter_dataMatrix.tsv --- a/tools/w4mclassfilter/test-data/input_nofilter_dataMatrix.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -dataMatrix HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_204 HU_208 -HMDB03193 76043 412165 44943 27242 436566 173175 242549 57066 559869 3732 339188 471368 262271 127285 451270 212500 79673 NA 891129 43907 -HMDB01101 30689 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 891129 32742 -HMDB01101 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 72900 891129 30689 -HMDB10348 47259 544877 60885 34582 529874 168264 176500 76457 610110 16262 279156 524468 451573 591487 433529 161069 214392 13781 891129 39315 -HMDB59717 357351 1030464 301983 67604 306862 1028110 1530493 270027 1378535 289677 808334 1132813 871209 895435 715190 1563158 784738 146195 891129 239030 -HMDB00822 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 14627 -HMDB00299 250551 1046138 456162 159386 1013302 808657 614370 250403 768004 242085 504108 1014041 1362408 1057660 1110050 566050 411886 142233 891129 284775 -HMDB00191 560002 771533 575790 392284 888498 785428 645785 591569 960658 910201 639437 1092885 1409045 2292023 1246459 1945577 710519 773384 891129 622898 -HMDB00518 -34236 58249 85944 NA 342102 129886 175800 13154 230242 NA 440223 315368 10657 419508 48673 28361 514579 23108 891129 73831 -HMDB00715 1252089 2547452 905408 371059 4983588 5140022 2658555 814523 2558923 859466 4184204 3865723 3236644 2615560 3820724 3577833 2295288 625924 891129 1341900 -HMDB01032 2569205 26023086 1604999 430453 8103558 26222916 257139 675754 59906109 263055 31151730 18648127 14989438 1554658 20249262 5588731 871010 15920 891129 44276 -HMDB00208 747080 13420742 595872 1172376 7172632 3143654 4059767 1433702 5593888 5402629 2477288 3346077 4230072 7621236 8960828 10335722 7037373 1574738 891129 2540044 -HMDB04824 374028 1144386 539206 178517 1046190 959381 605191 310260 1253319 477259 477995 825691 1157093 1089284 1411802 1020206 782673 346761 891129 387811 -HMDB00512 NA 319783 280560 85009 1333877 556003 590779 209285 342532 198512 569970 525240 246282 1140422 542345 1171008 827723 222953 891129 85554 -HMDB00251 368600 616555 94936 622468 180988 293988 352855 767894 268331 167246 310918 1248919 577184 10985 335711 403815 80614 63393 891129 616061 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/input_sampleMetadata.tsv --- a/tools/w4mclassfilter/test-data/input_sampleMetadata.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -sampleMetadata injectionOrder mode age bmi gender -HU_017 2 pos 41 23.03 M -HU_028 7 pos 41 23.92 F -HU_034 9 pos 52 23.37 M -HU_051 20 pos 24 23.23 F -HU_060 24 pos 55 28.72 F -HU_078 34 pos 46 25.18 M -HU_091 42 pos 61 26.12 M -HU_093 43 pos 53 21.71 M -HU_099 46 pos 23 21.3 M -HU_110 53 pos 50 20.9 F -HU_130 63 pos 33 26.06 M -HU_134 67 pos 48 22.89 M -HU_138 68 pos 42 21.88 M -HU_149 72 pos 35 19.49 F -HU_152 75 pos 26 17.58 F -HU_175 87 pos 35 21.26 F -HU_178 88 pos 60 32.87 F -HU_185 95 pos 42 21.09 F -HU_204 104 pos 31 29.06 M -HU_208 106 pos 27 18.61 F diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/input_variableMetadata.tsv --- a/tools/w4mclassfilter/test-data/input_variableMetadata.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -variable name mz rt -HMDB03193 foo 100 200 -HMDB01101 bar 150 300 -HMDB01101 baz 200 225 -HMDB00208 loquimini 873 476 -HMDB10348 batur 300 275 -HMDB00299 bantur 700 500 -HMDB00191 loquor 650 600 -HMDB00518 loquoris 870 250 -HMDB59717 bamur 125 400 -HMDB00822 bamini 300 199 -HMDB13189 baris 800 325 -HMDB00715 loquitur 725 900 -HMDB01032 loquimur 550 425 -HMDB04824 loquantur 950 522 -HMDB00512 pantur 900 543 -HMDB00251 pasamur 500 423 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/rangefilter_dataMatrix.tsv --- a/tools/w4mclassfilter/test-data/rangefilter_dataMatrix.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_149 HU_152 HU_175 HU_178 HU_185 HU_208 -HMDB00191 19.0950724540801 19.5573683394871 19.1351832076319 18.581538968171 19.7610090032025 19.5831195045026 19.3006944055142 19.1741869272827 19.8736633887651 19.7958256457729 19.2864427002132 21.1281900906526 20.2494039981067 20.8917666482316 19.438513703552 19.5608253922588 19.2486364146654 -HMDB00208 19.5109032146715 23.6779611010349 19.1846429313023 20.1610039089984 22.7740711828923 21.5840110083096 21.9529654992985 20.451313755289 22.4154199380002 22.3652301844309 21.2403301698498 22.8615935600174 23.0952006159265 23.3011358356974 22.746605551146 20.5866803867983 21.2764220576728 -HMDB01032 21.2928905785523 24.6332887213057 20.6141409677961 18.7154961966847 22.9501240553341 24.6443247870262 17.9721889132336 19.3661386209868 25.8361997953493 18.0050049466979 24.8928089492302 20.5681658146509 24.2713659930314 22.4140893053724 19.7323297568288 13.958552715431 15.4342372710269 -HMDB01101.1 22.7134708439962 15.6722319530667 11.6247954558602 23.3631578345615 17.8085620299575 22.183613575742 21.8871689158671 19.8971659609365 19.6661147561338 19.214418735272 20.6142092807528 20.079142288524 20.4818181509538 14.9315685693242 21.3775881248719 16.1536311941017 14.9054340159519 -HMDB13189 21.3346290086766 19.4727602406215 20.6639784491577 19.2400016764968 17.0561931543153 21.3938481405109 19.1797706242895 19.6763582845664 21.7496566885488 20.9339312108399 20.6175661105571 16.7978767996065 21.5788388647145 21.4643567902489 20.9969706149343 19.9807336965562 19.6828797432404 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/rangefilter_sampleMetadata.tsv --- a/tools/w4mclassfilter/test-data/rangefilter_sampleMetadata.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -sampleMetadata injectionOrder mode age bmi gender -HU_017 2 pos 41 23.03 M -HU_028 7 pos 41 23.92 F -HU_034 9 pos 52 23.37 M -HU_051 20 pos 24 23.23 F -HU_060 24 pos 55 28.72 F -HU_078 34 pos 46 25.18 M -HU_091 42 pos 61 26.12 M -HU_093 43 pos 53 21.71 M -HU_099 46 pos 23 21.3 M -HU_110 53 pos 50 20.9 F -HU_130 63 pos 33 26.06 M -HU_149 72 pos 35 19.49 F -HU_152 75 pos 26 17.58 F -HU_175 87 pos 35 21.26 F -HU_178 88 pos 60 32.87 F -HU_185 95 pos 42 21.09 F -HU_208 106 pos 27 18.61 F diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test-data/rangefilter_variableMetadata.tsv --- a/tools/w4mclassfilter/test-data/rangefilter_variableMetadata.tsv Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -variableMetadata name mz rt -HMDB00191 loquor 650 600 -HMDB00208 loquimini 873 476 -HMDB01032 loquimur 550 425 -HMDB01101.1 baz 200 225 -HMDB13189 baris 800 325 diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/test_log.txt --- a/tools/w4mclassfilter/test_log.txt Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1670 +0,0 @@ -git --git-dir /home/rstudio/.planemo/gx_repo config remote.origin.fetch '+refs/*:refs/*' -git --git-dir /home/rstudio/.planemo/gx_repo config remote.origin.mirror true -git --git-dir /home/rstudio/.planemo/gx_repo remote update >/dev/null 2>&1 -galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input -git clone --branch master /home/rstudio/.planemo/gx_repo /tmp/tmp0krucrv3/galaxy-dev -Cloning into '/tmp/tmp0krucrv3/galaxy-dev'... -done. -Updating files: 39% (2112/5412) Updating files: 40% (2165/5412) Updating files: 41% (2219/5412) Updating files: 42% (2274/5412) Updating files: 43% (2328/5412) Updating files: 44% (2382/5412) Updating files: 45% (2436/5412) Updating files: 46% (2490/5412) Updating files: 47% (2544/5412) Updating files: 48% (2598/5412) Updating files: 49% (2652/5412) Updating files: 50% (2706/5412) Updating files: 51% (2761/5412) Updating files: 52% 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(4438/5412) Updating files: 83% (4492/5412) Updating files: 84% (4547/5412) Updating files: 85% (4601/5412) Updating files: 86% (4655/5412) Updating files: 87% (4709/5412) Updating files: 88% (4763/5412) Updating files: 89% (4817/5412) Updating files: 90% (4871/5412) Updating files: 91% (4925/5412) Updating files: 92% (4980/5412) Updating files: 93% (5034/5412) Updating files: 94% (5088/5412) Updating files: 95% (5142/5412) Updating files: 96% (5196/5412) Updating files: 97% (5250/5412) Updating files: 98% (5304/5412) Updating files: 99% (5358/5412) Updating files: 100% (5412/5412) Updating files: 100% (5412/5412), done. -if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/rstudio/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/rstudio/venv/bin/virtualenv -p /home/rstudio/venv/bin/python3 $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}" && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS} -galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input -Activated a virtualenv for Galaxy -/home/rstudio/.planemo/gx_venv_3 -Set COMMON_STARTUP_ARGS to --dev-wheels -Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample -Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample -Initializing static/welcome.html from welcome.html.sample -Activating virtualenv at /home/rstudio/.planemo/gx_venv_3 -Requirement already satisfied: pip>=8.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (21.0.1) -Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple -Ignoring importlib-metadata: markers 'python_version < "3.8"' don't match your environment -Ignoring importlib-resources: markers 'python_version < "3.7"' don't match your environment -Ignoring pathlib2: markers 'python_version < "3.6"' don't match your environment -Ignoring ruamel.yaml.clib: markers 'platform_python_implementation == "CPython" and python_version < "3.8"' don't match your environment -Ignoring typing: markers 'python_version < "3.5"' don't match your environment -Ignoring zipp: markers 'python_version < "3.8"' don't match your environment -Ignoring importlib-metadata: markers 'python_version < "3.8"' don't match your environment -Ignoring pathlib2: markers 'python_version < "3.6"' don't match your environment -Ignoring zipp: markers 'python_version < "3.8"' don't match your environment -Requirement already satisfied: adal==1.2.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 3)) (1.2.4) -Requirement already satisfied: amqp==2.6.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 4)) (2.6.0) -Requirement already satisfied: appdirs==1.4.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 5)) (1.4.4) -Requirement already satisfied: attmap==0.12.11 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 6)) (0.12.11) -Requirement already satisfied: attrs==19.3.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 7)) (19.3.0) -Requirement already satisfied: azure-common==1.1.14 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 8)) (1.1.14) -Requirement already satisfied: azure-cosmosdb-nspkg==2.0.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 9)) (2.0.2) -Requirement already satisfied: azure-cosmosdb-table==1.0.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 10)) (1.0.4) -Requirement already satisfied: azure-mgmt-compute==4.0.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 11)) (4.0.1) -Requirement already satisfied: azure-mgmt-devtestlabs==2.2.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 12)) (2.2.0) -Requirement already satisfied: azure-mgmt-network==2.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 13)) (2.1.0) -Requirement already satisfied: azure-mgmt-nspkg==3.0.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 14)) (3.0.2) -Requirement already satisfied: azure-mgmt-resource==2.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 15)) (2.0.0) -Requirement already satisfied: azure-mgmt-storage==2.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 16)) (2.0.0) -Requirement already satisfied: azure-nspkg==3.0.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 17)) (3.0.2) -Requirement already satisfied: azure-storage-blob==1.3.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 18)) (1.3.1) -Requirement already satisfied: azure-storage-common==1.4.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 19)) (1.4.2) -Requirement already satisfied: azure-storage-nspkg==3.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 20)) (3.1.0) -Requirement already satisfied: babel==2.8.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 21)) (2.8.0) -Requirement already satisfied: bagit==1.7.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 22)) (1.7.0) -Requirement already satisfied: bcrypt==3.1.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 23)) (3.1.7) -Requirement already satisfied: bdbag==1.5.6 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 24)) (1.5.6) -Requirement already satisfied: beaker==1.11.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 25)) (1.11.0) -Requirement already satisfied: bioblend==0.13.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 26)) (0.13.0) -Requirement already satisfied: bleach==3.1.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 27)) (3.1.5) -Requirement already satisfied: boltons==20.2.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 28)) (20.2.0) -Requirement already satisfied: boto3==1.9.114 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 29)) (1.9.114) -Requirement already satisfied: boto==2.49.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 30)) (2.49.0) -Requirement already satisfied: botocore==1.12.253 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 31)) (1.12.253) -Requirement already satisfied: bx-python==0.8.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 32)) (0.8.9) -Requirement already satisfied: cachecontrol==0.11.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 33)) (0.11.7) -Requirement already satisfied: cachetools==4.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 34)) (4.1.0) -Requirement already satisfied: certifi==2020.6.20 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 35)) (2020.6.20) -Requirement already satisfied: cffi==1.14.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 36)) (1.14.0) -Requirement already satisfied: chardet==3.0.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 37)) (3.0.4) -Requirement already satisfied: cheetah3==3.2.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 38)) (3.2.5) -Requirement already satisfied: cliff==3.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 39)) (3.1.0) -Requirement already satisfied: cloudauthz==0.6.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 40)) (0.6.0) -Requirement already satisfied: cloudbridge==2.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 41)) (2.0.0) -Requirement already satisfied: cmd2==0.8.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 42)) (0.8.9) -Requirement already satisfied: coloredlogs==14.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 43)) (14.0) -Requirement already satisfied: cryptography==3.2.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 44)) (3.2.1) -Requirement already satisfied: cwltool==1.0.20191225192155 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 45)) (1.0.20191225192155) -Requirement already satisfied: debtcollector==1.22.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 46)) (1.22.0) -Requirement already satisfied: decorator==4.4.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 47)) (4.4.2) -Requirement already satisfied: defusedxml==0.6.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 48)) (0.6.0) -Requirement already satisfied: deprecated==1.2.10 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 49)) (1.2.10) -Requirement already satisfied: deprecation==2.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 50)) (2.1.0) -Requirement already satisfied: dictobj==0.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 51)) (0.4) -Requirement already satisfied: docopt==0.6.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 52)) (0.6.2) -Requirement already satisfied: docutils==0.15.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 53)) (0.15.2) -Requirement already satisfied: dogpile.cache==0.9.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 54)) (0.9.2) -Requirement already satisfied: ecdsa==0.15 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 55)) (0.15) -Requirement already satisfied: fabric3==1.14.post1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 56)) (1.14.post1) -Requirement already satisfied: future==0.18.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 57)) (0.18.2) -Requirement already satisfied: futures==3.1.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 58)) (3.1.1) -Requirement already satisfied: galaxy-sequence-utils==1.1.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 59)) (1.1.5) -Requirement already satisfied: google-api-python-client==1.7.8 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 60)) (1.7.8) -Requirement already satisfied: google-auth-httplib2==0.0.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 61)) (0.0.3) -Requirement already satisfied: google-auth==1.18.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 62)) (1.18.0) -Requirement already satisfied: gxformat2==0.11.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 63)) (0.11.3) -Requirement already satisfied: h5py==2.10.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 64)) (2.10.0) -Requirement already satisfied: httplib2==0.18.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 65)) (0.18.1) -Requirement already satisfied: humanfriendly==8.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 66)) (8.2) -Requirement already satisfied: idna==2.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 67)) (2.9) -Requirement already satisfied: isa-rwval==0.10.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 70)) (0.10.9) -Requirement already satisfied: iso8601==0.1.12 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 71)) (0.1.12) -Requirement already satisfied: isodate==0.6.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 72)) (0.6.0) -Requirement already satisfied: jmespath==0.10.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 73)) (0.10.0) -Requirement already satisfied: jsonpatch==1.26 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 74)) (1.26) -Requirement already satisfied: jsonpointer==2.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 75)) (2.0) -Requirement already satisfied: jsonschema==3.2.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 76)) (3.2.0) -Requirement already satisfied: keystoneauth1==4.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 77)) (4.1.0) -Requirement already satisfied: kombu==4.6.11 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 78)) (4.6.11) -Requirement already satisfied: lockfile==0.12.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 79)) (0.12.2) -Requirement already satisfied: lxml==4.6.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 80)) (4.6.2) -Requirement already satisfied: mako==1.1.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 81)) (1.1.3) -Requirement already satisfied: markdown==3.2.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 82)) (3.2.2) -Requirement already satisfied: markupsafe==1.1.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 83)) (1.1.1) -Requirement already satisfied: mercurial==5.4.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 84)) (5.4.1) -Requirement already satisfied: mistune==0.8.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 85)) (0.8.4) -Requirement already satisfied: msgpack==1.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 86)) (1.0.0) -Requirement already satisfied: msrest==0.5.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 87)) (0.5.5) -Requirement already satisfied: msrestazure==0.5.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 88)) (0.5.0) -Requirement already satisfied: munch==2.5.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 89)) (2.5.0) -Requirement already satisfied: mypy-extensions==0.4.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 90)) (0.4.3) -Requirement already satisfied: netaddr==0.7.20 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 91)) (0.7.20) -Requirement already satisfied: netifaces==0.10.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 92)) (0.10.9) -Requirement already satisfied: networkx==1.11 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 93)) (1.11) -Requirement already satisfied: nodeenv==1.4.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 94)) (1.4.0) -Requirement already satisfied: nose==1.3.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 95)) (1.3.7) -Requirement already satisfied: numpy==1.18.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 96)) (1.18.5) -Requirement already satisfied: oauth2client==4.1.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 97)) (4.1.3) -Requirement already satisfied: oauthlib==3.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 98)) (3.1.0) -Requirement already satisfied: openstacksdk==0.17.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 99)) (0.17.0) -Requirement already satisfied: os-client-config==2.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 100)) (2.1.0) -Requirement already satisfied: os-service-types==1.7.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 101)) (1.7.0) -Requirement already satisfied: osc-lib==2.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 102)) (2.0.0) -Requirement already satisfied: oslo.config==7.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 103)) (7.0.0) -Requirement already satisfied: oslo.context==2.23.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 104)) (2.23.1) -Requirement already satisfied: oslo.i18n==3.25.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 105)) (3.25.1) -Requirement already satisfied: oslo.log==3.45.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 106)) (3.45.2) -Requirement already satisfied: oslo.serialization==2.29.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 107)) (2.29.2) -Requirement already satisfied: oslo.utils==3.42.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 108)) (3.42.1) -Requirement already satisfied: oyaml==0.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 109)) (0.9) -Requirement already satisfied: packaging==20.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 110)) (20.4) -Requirement already satisfied: paramiko==2.7.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 111)) (2.7.1) -Requirement already satisfied: parsley==1.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 112)) (1.3) -Requirement already satisfied: paste==3.4.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 113)) (3.4.1) -Requirement already satisfied: pastedeploy==2.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 114)) (2.1.0) -Requirement already satisfied: pastescript==3.2.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 115)) (3.2.0) -Requirement already satisfied: pbr==5.4.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 117)) (5.4.5) -Requirement already satisfied: prettytable==0.7.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 118)) (0.7.2) -Requirement already satisfied: prov==1.5.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 119)) (1.5.1) -Requirement already satisfied: psutil==5.7.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 120)) (5.7.0) -Requirement already satisfied: pulsar-galaxy-lib==0.14.0.dev4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 121)) (0.14.0.dev4) -Requirement already satisfied: pyasn1-modules==0.2.8 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 122)) (0.2.8) -Requirement already satisfied: pyasn1==0.4.8 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 123)) (0.4.8) -Requirement already satisfied: pycparser==2.20 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 124)) (2.20) -Requirement already satisfied: pycryptodome==3.9.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 125)) (3.9.7) -Requirement already satisfied: pyeventsystem==0.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 126)) (0.1.0) -Requirement already satisfied: pyinotify==0.9.6 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 127)) (0.9.6) -Requirement already satisfied: pyjwt==1.7.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 128)) (1.7.1) -Requirement already satisfied: pykwalify==1.7.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 129)) (1.7.0) -Requirement already satisfied: pynacl==1.4.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 130)) (1.4.0) -Requirement already satisfied: pyopenssl==19.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 131)) (19.1.0) -Requirement already satisfied: pyparsing==2.4.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 132)) (2.4.7) -Requirement already satisfied: pyperclip==1.8.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 133)) (1.8.0) -Requirement already satisfied: pyrsistent==0.16.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 134)) (0.16.0) -Requirement already satisfied: pysam==0.16.0.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 135)) (0.16.0.1) -Requirement already satisfied: pysftp==0.2.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 136)) (0.2.9) -Requirement already satisfied: python-cinderclient==4.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 137)) (4.0.0) -Requirement already satisfied: python-dateutil==2.8.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 138)) (2.8.1) -Requirement already satisfied: python-glanceclient==2.12.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 139)) (2.12.0) -Requirement already satisfied: python-jose==3.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 140)) (3.1.0) -Requirement already satisfied: python-keystoneclient==3.17.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 141)) (3.17.0) -Requirement already satisfied: python-neutronclient==6.9.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 142)) (6.9.0) -Requirement already satisfied: python-novaclient==11.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 143)) (11.0.0) -Requirement already satisfied: python-swiftclient==3.6.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 144)) (3.6.0) -Requirement already satisfied: python3-openid==3.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 145)) (3.1.0) -Requirement already satisfied: pytz==2020.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 146)) (2020.1) -Requirement already satisfied: pyuwsgi==2.0.19.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 147)) (2.0.19.1) -Requirement already satisfied: pyyaml==5.3.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 148)) (5.3.1) -Requirement already satisfied: rdflib-jsonld==0.4.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 149)) (0.4.0) -Requirement already satisfied: rdflib==4.2.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 150)) (4.2.2) -Requirement already satisfied: refgenconf==0.7.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 151)) (0.7.0) -Requirement already satisfied: repoze.lru==0.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 152)) (0.7) -Requirement already satisfied: requests-oauthlib==1.3.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 153)) (1.3.0) -Requirement already satisfied: requests-toolbelt==0.9.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 154)) (0.9.1) -Requirement already satisfied: requests==2.24.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 155)) (2.24.0) -Requirement already satisfied: requestsexceptions==1.4.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 156)) (1.4.0) -Requirement already satisfied: rfc3986==1.4.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 157)) (1.4.0) -Requirement already satisfied: routes==2.4.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 158)) (2.4.1) -Requirement already satisfied: rsa==4.6 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 159)) (4.6) -Requirement already satisfied: ruamel.yaml==0.16.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 161)) (0.16.0) -Requirement already satisfied: s3transfer==0.2.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 162)) (0.2.1) -Requirement already satisfied: scandir==1.10.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 163)) (1.10.0) -Requirement already satisfied: schema-salad==4.5.20191229160203 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 164)) (4.5.20191229160203) -Requirement already satisfied: setuptools-scm==4.1.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 165)) (4.1.2) -Requirement already satisfied: shellescape==3.4.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 166)) (3.4.1) -Requirement already satisfied: simplejson==3.17.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 167)) (3.17.0) -Requirement already satisfied: six==1.15.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 168)) (1.15.0) -Requirement already satisfied: social-auth-core[openidconnect]==3.3.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 169)) (3.3.0) -Requirement already satisfied: sortedcontainers==2.2.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 170)) (2.2.2) -Requirement already satisfied: sqlalchemy-migrate==0.13.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 171)) (0.13.0) -Requirement already satisfied: sqlalchemy-utils==0.36.6 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 172)) (0.36.6) -Requirement already satisfied: sqlalchemy==1.3.17 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 173)) (1.3.17) -Requirement already satisfied: sqlitedict==1.7.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 174)) (1.7.0) -Requirement already satisfied: sqlparse==0.3.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 175)) (0.3.1) -Requirement already satisfied: stevedore==1.32.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 176)) (1.32.0) -Requirement already satisfied: svgwrite==1.3.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 177)) (1.3.1) -Requirement already satisfied: tempita==0.5.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 178)) (0.5.2) -Requirement already satisfied: tenacity==4.12.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 179)) (4.12.0) -Requirement already satisfied: tqdm==4.46.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 180)) (4.46.1) -Requirement already satisfied: typing-extensions==3.7.4.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 181)) (3.7.4.2) -Requirement already satisfied: tzlocal==2.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 183)) (2.1) -Requirement already satisfied: ubiquerg==0.5.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 184)) (0.5.2) -Requirement already satisfied: unidecode==1.1.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 185)) (1.1.1) -Requirement already satisfied: uritemplate==3.0.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 186)) (3.0.1) -Requirement already satisfied: urllib3==1.25.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 187)) (1.25.9) -Requirement already satisfied: vine==1.3.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 188)) (1.3.0) -Requirement already satisfied: warlock==1.3.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 189)) (1.3.3) -Requirement already satisfied: wcwidth==0.2.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 190)) (0.2.5) -Requirement already satisfied: webencodings==0.5.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 191)) (0.5.1) -Requirement already satisfied: webob==1.8.6 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 192)) (1.8.6) -Requirement already satisfied: whoosh==2.7.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 193)) (2.7.4) -Requirement already satisfied: wrapt==1.12.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 194)) (1.12.1) -Requirement already satisfied: yacman==0.6.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 195)) (0.6.7) -Requirement already satisfied: alabaster==0.7.12 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) (0.7.12) -Requirement already satisfied: commonmark==0.9.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 8)) (0.9.1) -Requirement already satisfied: coverage==5.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 9)) (5.1) -Requirement already satisfied: gunicorn==20.0.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 12)) (20.0.4) -Requirement already satisfied: imagesize==1.2.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 14)) (1.2.0) -Requirement already satisfied: jinja2==2.11.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 16)) (2.11.2) -Requirement already satisfied: mirakuru==2.0.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 20)) (2.0.2) -Requirement already satisfied: mock==3.0.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 21)) (3.0.5) -Requirement already satisfied: more-itertools==8.4.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 22)) (8.4.0) -Requirement already satisfied: nosehtml==0.4.6 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 24)) (0.4.6) -Requirement already satisfied: pathtools==0.1.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (0.1.2) -Requirement already satisfied: pluggy==0.13.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 28)) (0.13.1) -Requirement already satisfied: port-for==0.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 29)) (0.4) -Requirement already satisfied: py==1.8.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 32)) (1.8.2) -Requirement already satisfied: pygithub==1.51 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 33)) (1.51) -Requirement already satisfied: pygments==2.6.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 34)) (2.6.1) -Requirement already satisfied: pytest-cov==2.10.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 37)) (2.10.0) -Requirement already satisfied: pytest-html==1.22.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 38)) (1.22.1) -Requirement already satisfied: pytest-metadata==1.8.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 39)) (1.8.0) -Requirement already satisfied: pytest-mock==3.1.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 40)) (3.1.1) -Requirement already satisfied: pytest-postgresql==2.3.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 41)) (2.3.0) -Requirement already satisfied: pytest-pythonpath==0.7.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 42)) (0.7.3) -Requirement already satisfied: pytest==5.4.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 43)) (5.4.3) -Requirement already satisfied: python-irodsclient==0.8.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (0.8.3) -Requirement already satisfied: recommonmark==0.6.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 46)) (0.6.0) -Requirement already satisfied: responses==0.10.15 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 48)) (0.10.15) -Requirement already satisfied: selenium==3.141.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 49)) (3.141.0) -Requirement already satisfied: snowballstemmer==2.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (2.0.0) -Requirement already satisfied: sphinx-markdown-tables==0.0.15 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 52)) (0.0.15) -Requirement already satisfied: sphinx-rtd-theme==0.5.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 53)) (0.5.0) -Requirement already satisfied: sphinx==3.1.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 54)) (3.1.1) -Requirement already satisfied: sphinxcontrib-applehelp==1.0.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55)) (1.0.2) -Requirement already satisfied: sphinxcontrib-devhelp==1.0.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 56)) (1.0.2) -Requirement already satisfied: sphinxcontrib-htmlhelp==1.0.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 57)) (1.0.3) -Requirement already satisfied: sphinxcontrib-jsmath==1.0.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 58)) (1.0.1) -Requirement already satisfied: sphinxcontrib-qthelp==1.0.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 59)) (1.0.3) -Requirement already satisfied: sphinxcontrib-serializinghtml==1.1.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 60)) (1.1.4) -Requirement already satisfied: testfixtures==6.14.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 61)) (6.14.1) -Requirement already satisfied: twill==2.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 62)) (2.0) -Requirement already satisfied: watchdog==0.10.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 64)) (0.10.2) -Requirement already satisfied: xmlrunner==1.7.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 67)) (1.7.7) -Requirement already satisfied: setuptools in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 45)) (52.0.0) -Requirement already satisfied: pathlib2!=2.3.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 45)) (2.3.5) -The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable. -Testing using galaxy_root /tmp/tmp0krucrv3/galaxy-dev -Testing tools with command [cd /tmp/tmp0krucrv3/galaxy-dev && if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/rstudio/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/rstudio/venv/bin/virtualenv -p /home/rstudio/venv/bin/python3 $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./run_tests.sh $COMMON_STARTUP_ARGS --report_file /home/rstudio/src/w4mclassfilter_galaxy_wrapper/tools/w4mclassfilter/tool_test_output.html --xunit_report_file /tmp/tmp0krucrv3/xunit.xml --structured_data_report_file /home/rstudio/src/w4mclassfilter_galaxy_wrapper/tools/w4mclassfilter/tool_test_output.json functional.test_toolbox] -galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input -Activated a virtualenv for Galaxy -/home/rstudio/.planemo/gx_venv_3 -Activating virtualenv at /home/rstudio/.planemo/gx_venv_3 -Requirement already satisfied: pip>=8.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (21.0.1) -Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple -Ignoring importlib-metadata: markers 'python_version < "3.8"' don't match your environment -Ignoring importlib-resources: markers 'python_version < "3.7"' don't match your environment -Ignoring pathlib2: markers 'python_version < "3.6"' don't match your environment -Ignoring ruamel.yaml.clib: markers 'platform_python_implementation == "CPython" and python_version < "3.8"' don't match your environment -Ignoring typing: markers 'python_version < "3.5"' don't match your environment -Ignoring zipp: markers 'python_version < "3.8"' don't match your environment -Ignoring importlib-metadata: markers 'python_version < "3.8"' don't match your environment -Ignoring pathlib2: markers 'python_version < "3.6"' don't match your environment -Ignoring zipp: markers 'python_version < "3.8"' don't match your environment -Requirement already satisfied: adal==1.2.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 3)) (1.2.4) -Requirement already satisfied: amqp==2.6.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 4)) (2.6.0) -Requirement already satisfied: appdirs==1.4.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 5)) (1.4.4) -Requirement already satisfied: attmap==0.12.11 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 6)) (0.12.11) -Requirement already satisfied: attrs==19.3.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 7)) (19.3.0) -Requirement already satisfied: azure-common==1.1.14 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 8)) (1.1.14) -Requirement already satisfied: azure-cosmosdb-nspkg==2.0.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 9)) (2.0.2) -Requirement already satisfied: azure-cosmosdb-table==1.0.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 10)) (1.0.4) -Requirement already satisfied: azure-mgmt-compute==4.0.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 11)) (4.0.1) -Requirement already satisfied: azure-mgmt-devtestlabs==2.2.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 12)) (2.2.0) -Requirement already satisfied: azure-mgmt-network==2.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 13)) (2.1.0) -Requirement already satisfied: azure-mgmt-nspkg==3.0.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 14)) (3.0.2) -Requirement already satisfied: azure-mgmt-resource==2.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 15)) (2.0.0) -Requirement already satisfied: azure-mgmt-storage==2.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 16)) (2.0.0) -Requirement already satisfied: azure-nspkg==3.0.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 17)) (3.0.2) -Requirement already satisfied: azure-storage-blob==1.3.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 18)) (1.3.1) -Requirement already satisfied: azure-storage-common==1.4.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 19)) (1.4.2) -Requirement already satisfied: azure-storage-nspkg==3.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 20)) (3.1.0) -Requirement already satisfied: babel==2.8.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 21)) (2.8.0) -Requirement already satisfied: bagit==1.7.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 22)) (1.7.0) -Requirement already satisfied: bcrypt==3.1.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 23)) (3.1.7) -Requirement already satisfied: bdbag==1.5.6 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 24)) (1.5.6) -Requirement already satisfied: beaker==1.11.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 25)) (1.11.0) -Requirement already satisfied: bioblend==0.13.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 26)) (0.13.0) -Requirement already satisfied: bleach==3.1.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 27)) (3.1.5) -Requirement already satisfied: boltons==20.2.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 28)) (20.2.0) -Requirement already satisfied: boto3==1.9.114 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 29)) (1.9.114) -Requirement already satisfied: boto==2.49.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 30)) (2.49.0) -Requirement already satisfied: botocore==1.12.253 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 31)) (1.12.253) -Requirement already satisfied: bx-python==0.8.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 32)) (0.8.9) -Requirement already satisfied: cachecontrol==0.11.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 33)) (0.11.7) -Requirement already satisfied: cachetools==4.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 34)) (4.1.0) -Requirement already satisfied: certifi==2020.6.20 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 35)) (2020.6.20) -Requirement already satisfied: cffi==1.14.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 36)) (1.14.0) -Requirement already satisfied: chardet==3.0.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 37)) (3.0.4) -Requirement already satisfied: cheetah3==3.2.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 38)) (3.2.5) -Requirement already satisfied: cliff==3.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 39)) (3.1.0) -Requirement already satisfied: cloudauthz==0.6.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 40)) (0.6.0) -Requirement already satisfied: cloudbridge==2.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 41)) (2.0.0) -Requirement already satisfied: cmd2==0.8.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 42)) (0.8.9) -Requirement already satisfied: coloredlogs==14.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 43)) (14.0) -Requirement already satisfied: cryptography==3.2.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 44)) (3.2.1) -Requirement already satisfied: cwltool==1.0.20191225192155 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 45)) (1.0.20191225192155) -Requirement already satisfied: debtcollector==1.22.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 46)) (1.22.0) -Requirement already satisfied: decorator==4.4.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 47)) (4.4.2) -Requirement already satisfied: defusedxml==0.6.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 48)) (0.6.0) -Requirement already satisfied: deprecated==1.2.10 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 49)) (1.2.10) -Requirement already satisfied: deprecation==2.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 50)) (2.1.0) -Requirement already satisfied: dictobj==0.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 51)) (0.4) -Requirement already satisfied: docopt==0.6.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 52)) (0.6.2) -Requirement already satisfied: docutils==0.15.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 53)) (0.15.2) -Requirement already satisfied: dogpile.cache==0.9.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 54)) (0.9.2) -Requirement already satisfied: ecdsa==0.15 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 55)) (0.15) -Requirement already satisfied: fabric3==1.14.post1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 56)) (1.14.post1) -Requirement already satisfied: future==0.18.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 57)) (0.18.2) -Requirement already satisfied: futures==3.1.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 58)) (3.1.1) -Requirement already satisfied: galaxy-sequence-utils==1.1.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 59)) (1.1.5) -Requirement already satisfied: google-api-python-client==1.7.8 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 60)) (1.7.8) -Requirement already satisfied: google-auth-httplib2==0.0.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 61)) (0.0.3) -Requirement already satisfied: google-auth==1.18.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 62)) (1.18.0) -Requirement already satisfied: gxformat2==0.11.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 63)) (0.11.3) -Requirement already satisfied: h5py==2.10.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 64)) (2.10.0) -Requirement already satisfied: httplib2==0.18.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 65)) (0.18.1) -Requirement already satisfied: humanfriendly==8.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 66)) (8.2) -Requirement already satisfied: idna==2.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 67)) (2.9) -Requirement already satisfied: isa-rwval==0.10.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 70)) (0.10.9) -Requirement already satisfied: iso8601==0.1.12 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 71)) (0.1.12) -Requirement already satisfied: isodate==0.6.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 72)) (0.6.0) -Requirement already satisfied: jmespath==0.10.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 73)) (0.10.0) -Requirement already satisfied: jsonpatch==1.26 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 74)) (1.26) -Requirement already satisfied: jsonpointer==2.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 75)) (2.0) -Requirement already satisfied: jsonschema==3.2.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 76)) (3.2.0) -Requirement already satisfied: keystoneauth1==4.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 77)) (4.1.0) -Requirement already satisfied: kombu==4.6.11 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 78)) (4.6.11) -Requirement already satisfied: lockfile==0.12.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 79)) (0.12.2) -Requirement already satisfied: lxml==4.6.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 80)) (4.6.2) -Requirement already satisfied: mako==1.1.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 81)) (1.1.3) -Requirement already satisfied: markdown==3.2.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 82)) (3.2.2) -Requirement already satisfied: markupsafe==1.1.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 83)) (1.1.1) -Requirement already satisfied: mercurial==5.4.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 84)) (5.4.1) -Requirement already satisfied: mistune==0.8.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 85)) (0.8.4) -Requirement already satisfied: msgpack==1.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 86)) (1.0.0) -Requirement already satisfied: msrest==0.5.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 87)) (0.5.5) -Requirement already satisfied: msrestazure==0.5.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 88)) (0.5.0) -Requirement already satisfied: munch==2.5.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 89)) (2.5.0) -Requirement already satisfied: mypy-extensions==0.4.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 90)) (0.4.3) -Requirement already satisfied: netaddr==0.7.20 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 91)) (0.7.20) -Requirement already satisfied: netifaces==0.10.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 92)) (0.10.9) -Requirement already satisfied: networkx==1.11 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 93)) (1.11) -Requirement already satisfied: nodeenv==1.4.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 94)) (1.4.0) -Requirement already satisfied: nose==1.3.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 95)) (1.3.7) -Requirement already satisfied: numpy==1.18.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 96)) (1.18.5) -Requirement already satisfied: oauth2client==4.1.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 97)) (4.1.3) -Requirement already satisfied: oauthlib==3.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 98)) (3.1.0) -Requirement already satisfied: openstacksdk==0.17.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 99)) (0.17.0) -Requirement already satisfied: os-client-config==2.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 100)) (2.1.0) -Requirement already satisfied: os-service-types==1.7.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 101)) (1.7.0) -Requirement already satisfied: osc-lib==2.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 102)) (2.0.0) -Requirement already satisfied: oslo.config==7.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 103)) (7.0.0) -Requirement already satisfied: oslo.context==2.23.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 104)) (2.23.1) -Requirement already satisfied: oslo.i18n==3.25.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 105)) (3.25.1) -Requirement already satisfied: oslo.log==3.45.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 106)) (3.45.2) -Requirement already satisfied: oslo.serialization==2.29.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 107)) (2.29.2) -Requirement already satisfied: oslo.utils==3.42.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 108)) (3.42.1) -Requirement already satisfied: oyaml==0.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 109)) (0.9) -Requirement already satisfied: packaging==20.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 110)) (20.4) -Requirement already satisfied: paramiko==2.7.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 111)) (2.7.1) -Requirement already satisfied: parsley==1.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 112)) (1.3) -Requirement already satisfied: paste==3.4.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 113)) (3.4.1) -Requirement already satisfied: pastedeploy==2.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 114)) (2.1.0) -Requirement already satisfied: pastescript==3.2.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 115)) (3.2.0) -Requirement already satisfied: pbr==5.4.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 117)) (5.4.5) -Requirement already satisfied: prettytable==0.7.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 118)) (0.7.2) -Requirement already satisfied: prov==1.5.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 119)) (1.5.1) -Requirement already satisfied: psutil==5.7.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 120)) (5.7.0) -Requirement already satisfied: pulsar-galaxy-lib==0.14.0.dev4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 121)) (0.14.0.dev4) -Requirement already satisfied: pyasn1-modules==0.2.8 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 122)) (0.2.8) -Requirement already satisfied: pyasn1==0.4.8 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 123)) (0.4.8) -Requirement already satisfied: pycparser==2.20 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 124)) (2.20) -Requirement already satisfied: pycryptodome==3.9.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 125)) (3.9.7) -Requirement already satisfied: pyeventsystem==0.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 126)) (0.1.0) -Requirement already satisfied: pyinotify==0.9.6 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 127)) (0.9.6) -Requirement already satisfied: pyjwt==1.7.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 128)) (1.7.1) -Requirement already satisfied: pykwalify==1.7.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 129)) (1.7.0) -Requirement already satisfied: pynacl==1.4.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 130)) (1.4.0) -Requirement already satisfied: pyopenssl==19.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 131)) (19.1.0) -Requirement already satisfied: pyparsing==2.4.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 132)) (2.4.7) -Requirement already satisfied: pyperclip==1.8.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 133)) (1.8.0) -Requirement already satisfied: pyrsistent==0.16.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 134)) (0.16.0) -Requirement already satisfied: pysam==0.16.0.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 135)) (0.16.0.1) -Requirement already satisfied: pysftp==0.2.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 136)) (0.2.9) -Requirement already satisfied: python-cinderclient==4.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 137)) (4.0.0) -Requirement already satisfied: python-dateutil==2.8.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 138)) (2.8.1) -Requirement already satisfied: python-glanceclient==2.12.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 139)) (2.12.0) -Requirement already satisfied: python-jose==3.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 140)) (3.1.0) -Requirement already satisfied: python-keystoneclient==3.17.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 141)) (3.17.0) -Requirement already satisfied: python-neutronclient==6.9.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 142)) (6.9.0) -Requirement already satisfied: python-novaclient==11.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 143)) (11.0.0) -Requirement already satisfied: python-swiftclient==3.6.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 144)) (3.6.0) -Requirement already satisfied: python3-openid==3.1.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 145)) (3.1.0) -Requirement already satisfied: pytz==2020.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 146)) (2020.1) -Requirement already satisfied: pyuwsgi==2.0.19.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 147)) (2.0.19.1) -Requirement already satisfied: pyyaml==5.3.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 148)) (5.3.1) -Requirement already satisfied: rdflib-jsonld==0.4.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 149)) (0.4.0) -Requirement already satisfied: rdflib==4.2.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 150)) (4.2.2) -Requirement already satisfied: refgenconf==0.7.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 151)) (0.7.0) -Requirement already satisfied: repoze.lru==0.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 152)) (0.7) -Requirement already satisfied: requests-oauthlib==1.3.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 153)) (1.3.0) -Requirement already satisfied: requests-toolbelt==0.9.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 154)) (0.9.1) -Requirement already satisfied: requests==2.24.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 155)) (2.24.0) -Requirement already satisfied: requestsexceptions==1.4.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 156)) (1.4.0) -Requirement already satisfied: rfc3986==1.4.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 157)) (1.4.0) -Requirement already satisfied: routes==2.4.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 158)) (2.4.1) -Requirement already satisfied: rsa==4.6 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 159)) (4.6) -Requirement already satisfied: ruamel.yaml==0.16.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 161)) (0.16.0) -Requirement already satisfied: s3transfer==0.2.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 162)) (0.2.1) -Requirement already satisfied: scandir==1.10.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 163)) (1.10.0) -Requirement already satisfied: schema-salad==4.5.20191229160203 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 164)) (4.5.20191229160203) -Requirement already satisfied: setuptools-scm==4.1.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 165)) (4.1.2) -Requirement already satisfied: shellescape==3.4.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 166)) (3.4.1) -Requirement already satisfied: simplejson==3.17.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 167)) (3.17.0) -Requirement already satisfied: six==1.15.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 168)) (1.15.0) -Requirement already satisfied: social-auth-core[openidconnect]==3.3.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 169)) (3.3.0) -Requirement already satisfied: sortedcontainers==2.2.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 170)) (2.2.2) -Requirement already satisfied: sqlalchemy-migrate==0.13.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 171)) (0.13.0) -Requirement already satisfied: sqlalchemy-utils==0.36.6 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 172)) (0.36.6) -Requirement already satisfied: sqlalchemy==1.3.17 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 173)) (1.3.17) -Requirement already satisfied: sqlitedict==1.7.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 174)) (1.7.0) -Requirement already satisfied: sqlparse==0.3.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 175)) (0.3.1) -Requirement already satisfied: stevedore==1.32.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 176)) (1.32.0) -Requirement already satisfied: svgwrite==1.3.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 177)) (1.3.1) -Requirement already satisfied: tempita==0.5.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 178)) (0.5.2) -Requirement already satisfied: tenacity==4.12.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 179)) (4.12.0) -Requirement already satisfied: tqdm==4.46.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 180)) (4.46.1) -Requirement already satisfied: typing-extensions==3.7.4.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 181)) (3.7.4.2) -Requirement already satisfied: tzlocal==2.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 183)) (2.1) -Requirement already satisfied: ubiquerg==0.5.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 184)) (0.5.2) -Requirement already satisfied: unidecode==1.1.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 185)) (1.1.1) -Requirement already satisfied: uritemplate==3.0.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 186)) (3.0.1) -Requirement already satisfied: urllib3==1.25.9 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 187)) (1.25.9) -Requirement already satisfied: vine==1.3.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 188)) (1.3.0) -Requirement already satisfied: warlock==1.3.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 189)) (1.3.3) -Requirement already satisfied: wcwidth==0.2.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 190)) (0.2.5) -Requirement already satisfied: webencodings==0.5.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 191)) (0.5.1) -Requirement already satisfied: webob==1.8.6 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 192)) (1.8.6) -Requirement already satisfied: whoosh==2.7.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 193)) (2.7.4) -Requirement already satisfied: wrapt==1.12.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 194)) (1.12.1) -Requirement already satisfied: yacman==0.6.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r requirements.txt (line 195)) (0.6.7) -Requirement already satisfied: alabaster==0.7.12 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) (0.7.12) -Requirement already satisfied: commonmark==0.9.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 8)) (0.9.1) -Requirement already satisfied: coverage==5.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 9)) (5.1) -Requirement already satisfied: gunicorn==20.0.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 12)) (20.0.4) -Requirement already satisfied: imagesize==1.2.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 14)) (1.2.0) -Requirement already satisfied: jinja2==2.11.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 16)) (2.11.2) -Requirement already satisfied: mirakuru==2.0.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 20)) (2.0.2) -Requirement already satisfied: mock==3.0.5 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 21)) (3.0.5) -Requirement already satisfied: more-itertools==8.4.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 22)) (8.4.0) -Requirement already satisfied: nosehtml==0.4.6 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 24)) (0.4.6) -Requirement already satisfied: pathtools==0.1.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (0.1.2) -Requirement already satisfied: pluggy==0.13.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 28)) (0.13.1) -Requirement already satisfied: port-for==0.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 29)) (0.4) -Requirement already satisfied: py==1.8.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 32)) (1.8.2) -Requirement already satisfied: pygithub==1.51 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 33)) (1.51) -Requirement already satisfied: pygments==2.6.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 34)) (2.6.1) -Requirement already satisfied: pytest-cov==2.10.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 37)) (2.10.0) -Requirement already satisfied: pytest-html==1.22.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 38)) (1.22.1) -Requirement already satisfied: pytest-metadata==1.8.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 39)) (1.8.0) -Requirement already satisfied: pytest-mock==3.1.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 40)) (3.1.1) -Requirement already satisfied: pytest-postgresql==2.3.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 41)) (2.3.0) -Requirement already satisfied: pytest-pythonpath==0.7.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 42)) (0.7.3) -Requirement already satisfied: pytest==5.4.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 43)) (5.4.3) -Requirement already satisfied: python-irodsclient==0.8.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 44)) (0.8.3) -Requirement already satisfied: recommonmark==0.6.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 46)) (0.6.0) -Requirement already satisfied: responses==0.10.15 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 48)) (0.10.15) -Requirement already satisfied: selenium==3.141.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 49)) (3.141.0) -Requirement already satisfied: snowballstemmer==2.0.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 51)) (2.0.0) -Requirement already satisfied: sphinx-markdown-tables==0.0.15 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 52)) (0.0.15) -Requirement already satisfied: sphinx-rtd-theme==0.5.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 53)) (0.5.0) -Requirement already satisfied: sphinx==3.1.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 54)) (3.1.1) -Requirement already satisfied: sphinxcontrib-applehelp==1.0.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55)) (1.0.2) -Requirement already satisfied: sphinxcontrib-devhelp==1.0.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 56)) (1.0.2) -Requirement already satisfied: sphinxcontrib-htmlhelp==1.0.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 57)) (1.0.3) -Requirement already satisfied: sphinxcontrib-jsmath==1.0.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 58)) (1.0.1) -Requirement already satisfied: sphinxcontrib-qthelp==1.0.3 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 59)) (1.0.3) -Requirement already satisfied: sphinxcontrib-serializinghtml==1.1.4 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 60)) (1.1.4) -Requirement already satisfied: testfixtures==6.14.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 61)) (6.14.1) -Requirement already satisfied: twill==2.0 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 62)) (2.0) -Requirement already satisfied: watchdog==0.10.2 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 64)) (0.10.2) -Requirement already satisfied: xmlrunner==1.7.7 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 67)) (1.7.7) -Requirement already satisfied: setuptools in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 45)) (52.0.0) -Requirement already satisfied: pathlib2!=2.3.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from cwltool==1.0.20191225192155->-r requirements.txt (line 45)) (2.3.5) -Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple -Requirement already satisfied: watchdog in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from -r /dev/stdin (line 1)) (0.10.2) -Requirement already satisfied: pathtools>=0.1.1 in /home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages (from watchdog->-r /dev/stdin (line 1)) (0.1.2) -The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable. -Activating virtualenv at /home/rstudio/.planemo/gx_venv_3 -2021-03-11 20:11:21,978 INFO [galaxy.queue_worker] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////tmp/tmplk7fd25x/tmpvfh2m4rj/tmp5ie9b69s/database/control.sqlite?isolation_level=IMMEDIATE -2021-03-11 20:11:22,004 INFO [galaxy.model.migrate.check] Creating database for URI [sqlite:////tmp/tmp0krucrv3/galaxy.sqlite?isolation_level=IMMEDIATE] -2021-03-11 20:11:22,279 INFO [galaxy.model.migrate.check] Creating new database from scratch, skipping migrations -2021-03-11 20:12:14,824 INFO [galaxy.config] Install database targetting Galaxy's database configuration. -2021-03-11 20:12:14,834 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/all_fasta.loc, reading sample -2021-03-11 20:12:14,835 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/bfast_indexes.loc, reading sample -2021-03-11 20:12:14,835 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/blastdb.loc, reading sample -2021-03-11 20:12:14,836 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/blastdb_p.loc, reading sample -2021-03-11 20:12:14,836 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/blastdb_d.loc, reading sample -2021-03-11 20:12:14,836 WARNI [galaxy.tools.data] Cannot find index file 'bwa_index.loc' for tool data table 'bwa_indexes' -2021-03-11 20:12:14,837 WARNI [galaxy.tools.data] Cannot find index file 'bwa_index_color.loc' for tool data table 'bwa_indexes_color' -2021-03-11 20:12:14,837 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/maf_index.loc, reading sample -2021-03-11 20:12:14,837 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/ngs_sim_fasta.loc, reading sample -2021-03-11 20:12:14,838 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/perm_base_index.loc, reading sample -2021-03-11 20:12:14,838 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/perm_color_index.loc, reading sample -2021-03-11 20:12:14,838 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/picard_index.loc, reading sample -2021-03-11 20:12:14,839 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/picard_index.loc, reading sample -2021-03-11 20:12:14,839 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/mosaik_index.loc, reading sample -2021-03-11 20:12:14,840 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/twobit.loc, reading sample -2021-03-11 20:12:15,049 WARNI [galaxy.tools.data] Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '' characters must be used to separate fields): - -2021-03-11 20:12:15,050 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/liftOver.loc, reading sample -2021-03-11 20:12:15,051 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/bam_iobio.loc, reading sample -2021-03-11 20:12:15,051 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/vcf_iobio.loc, reading sample -2021-03-11 20:12:15,052 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/biom_simple_display.loc, reading sample -2021-03-11 20:12:15,052 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/intermine_simple_display.loc, reading sample -2021-03-11 20:12:15,052 INFO [galaxy.tools.data] Could not find tool data /tmp/tmp0krucrv3/galaxy-dev/tool-data/icn3d_simple_display.loc, reading sample -2021-03-11 20:12:15,123 INFO [galaxy.web_stack.handlers] JobConfiguration: No job handler assignment method is set, defaulting to 'db-preassign', set the `assign_with` attribute on to override the default -2021-03-11 20:12:15,123 INFO [galaxy.jobs] Job handler assignment methods set to: db-preassign -2021-03-11 20:12:15,123 INFO [galaxy.jobs] Tag [_default_] handlers: main -2021-03-11 20:12:15,406 WARNI [galaxy.tools] The default shed tool config file (/tmp/tmp0krucrv3/galaxy-dev/lib/galaxy/config/sample/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file -2021-03-11 20:12:15,406 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp0krucrv3/tool_conf.xml -2021-03-11 20:12:15,431 WARNI [galaxy.tools] The default shed tool config file (/tmp/tmp0krucrv3/galaxy-dev/lib/galaxy/config/sample/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file -2021-03-11 20:12:15,432 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp0krucrv3/shed_tools_conf.xml -2021-03-11 20:12:15,432 WARNI [galaxy.tools] The default shed tool config file (/tmp/tmp0krucrv3/galaxy-dev/lib/galaxy/config/sample/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file -2021-03-11 20:12:15,432 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp0krucrv3/empty_tool_conf.xml -Error loading a set of Dynamic Display Application links: A format or a metadata can be defined for a DisplayApplicationParameter, but not both. -Error loading a set of Dynamic Display Application links: A format or a metadata can be defined for a DisplayApplicationParameter, but not both. -2021-03-11 20:12:15,923 INFO [galaxy.jobs] Handler 'main' will load all configured runner plugins -2021-03-11 20:12:15,978 INFO [galaxy.jobs.handler] job handler stop queue started -2021-03-11 20:12:15,992 INFO [galaxy.jobs.handler] job handler queue started -2021-03-11 20:12:15,996 INFO [galaxy.jobs.handler] job handler stop queue started -2021-03-11 20:12:16,015 INFO [galaxy.workflow.scheduling_manager] No workflow schedulers plugin config file defined, using default scheduler. -2021-03-11 20:12:16,032 INFO [galaxy.queue_worker] Binding and starting galaxy control worker for main -2021-03-11 20:12:16,045 INFO [galaxy.queue_worker] Queuing async task rebuild_toolbox_search_index for main. -2021-03-11 20:12:16,738 INFO [galaxy.app] Galaxy app startup finished (55061.985 ms) -2021-03-11 20:12:16,858 INFO [galaxy.queue_worker] Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. -2021-03-11 20:12:17,628 INFO [galaxy.web_stack] Galaxy server instance 'main' is running -/home/rstudio/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/sqltypes.py:660: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. - util.warn( -2021-03-11 20:12:18,358 INFO [galaxy.webapps.base.webapp] Session authenticated using Galaxy master api key -2021-03-11 20:12:18,369 INFO [galaxy.webapps.base.webapp] Session authenticated using Galaxy master api key -2021-03-11 20:12:18,667 INFO [galaxy.webapps.base.webapp] Session authenticated using Galaxy master api key -( w4mclassfilter ) > Test-1 ... 2021-03-11 20:12:19,013 INFO [galaxy.tools] Validated and populated state for tool request (19.948 ms) -2021-03-11 20:12:19,522 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 1 -2021-03-11 20:12:19,617 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=1,tool_id=upload1] (65.859 ms) -2021-03-11 20:12:19,617 INFO [galaxy.web_stack.handlers] (Job[id=1,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:12:19,629 INFO [galaxy.web_stack.handlers] (Job[id=1,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:12:20,668 INFO [galaxy.jobs.handler] (1) Job dispatched -2021-03-11 20:12:20,916 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/1/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/1/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/1/upload_params.json' '1:/tmp/tmp0krucrv3/job_working_directory/000/1/working/dataset_b7ba21f9-2372-4dd9-8201-a5806573af43_files:/tmp/tmp0krucrv3/files/b/7/b/dataset_b7ba21f9-2372-4dd9-8201-a5806573af43.dat'] -2021-03-11 20:12:25,989 INFO [galaxy.tools] Validated and populated state for tool request (17.857 ms) -2021-03-11 20:12:26,433 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 2 -2021-03-11 20:12:26,523 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=2,tool_id=upload1] (62.146 ms) -2021-03-11 20:12:26,523 INFO [galaxy.web_stack.handlers] (Job[id=2,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:12:26,531 INFO [galaxy.web_stack.handlers] (Job[id=2,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:12:27,205 INFO [galaxy.jobs.handler] (2) Job dispatched -2021-03-11 20:12:27,435 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/2/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/2/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/2/upload_params.json' '2:/tmp/tmp0krucrv3/job_working_directory/000/2/working/dataset_c409b99b-2a57-403a-8125-083ca48b8faa_files:/tmp/tmp0krucrv3/files/c/4/0/dataset_c409b99b-2a57-403a-8125-083ca48b8faa.dat'] -2021-03-11 20:12:32,608 INFO [galaxy.tools] Validated and populated state for tool request (17.505 ms) -2021-03-11 20:12:33,042 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 3 -2021-03-11 20:12:33,119 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=3,tool_id=upload1] (55.813 ms) -2021-03-11 20:12:33,119 INFO [galaxy.web_stack.handlers] (Job[id=3,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:12:33,130 INFO [galaxy.web_stack.handlers] (Job[id=3,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:12:33,848 INFO [galaxy.jobs.handler] (3) Job dispatched -2021-03-11 20:12:34,077 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/3/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/3/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/3/upload_params.json' '3:/tmp/tmp0krucrv3/job_working_directory/000/3/working/dataset_35824d47-ff35-4566-8cf2-099777b9144f_files:/tmp/tmp0krucrv3/files/3/5/8/dataset_35824d47-ff35-4566-8cf2-099777b9144f.dat'] -2021-03-11 20:12:39,163 INFO [galaxy.tools] Validated and populated state for tool request (28.357 ms) -2021-03-11 20:12:39,248 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool w4mclassfilter (2.345 ms) -2021-03-11 20:12:39,250 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool w4mclassfilter (1.550 ms) -2021-03-11 20:12:39,252 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool w4mclassfilter (2.029 ms) -2021-03-11 20:12:39,252 INFO [galaxy.tools.actions] Added output datasets to history (0.054 ms) -2021-03-11 20:12:39,254 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=w4mclassfilter] complete, ready to be enqueued (1.728 ms) -2021-03-11 20:12:39,431 INFO [galaxy.web_stack.handlers] (Job[id=4,tool_id=w4mclassfilter]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:12:40,523 INFO [galaxy.jobs.handler] (4) Job dispatched -2021-03-11 20:12:40,775 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/4/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; unset R_HOME; if [ 'none' == 'medoid' -a 'zero' == 'none' ]; then (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2); [ ! 1 ]; else Rscript /home/rstudio/.planemo/planemo_tmp_ahme9v2m/w4mclassfilter_wrapper.R dataMatrix_in '/tmp/tmp0krucrv3/files/b/7/b/dataset_b7ba21f9-2372-4dd9-8201-a5806573af43.dat' sampleMetadata_in '/tmp/tmp0krucrv3/files/c/4/0/dataset_c409b99b-2a57-403a-8125-083ca48b8faa.dat' variableMetadata_in '/tmp/tmp0krucrv3/files/3/5/8/dataset_35824d47-ff35-4566-8cf2-099777b9144f.dat' sampleclassNames 'M' inclusive 'TRUE' wildcards 'FALSE' classnameColumn 'gender' samplenameColumn 'sampleMetadata' variable_range_filter 'FEATMAX:2e6:,mz:200:,rt::800' transformation 'none' imputation 'zero' dataMatrix_out '/tmp/tmp0krucrv3/files/4/a/5/dataset_4a526f7c-d781-428f-86c7-c280810fdada.dat' sampleMetadata_out '/tmp/tmp0krucrv3/files/d/5/9/dataset_d5926dee-18f0-43fd-85e3-074664cda8be.dat' variableMetadata_out '/tmp/tmp0krucrv3/files/b/d/c/dataset_bdcc61e1-d3a9-4890-9042-ca11c2c07d1b.dat' order_vrbl 'variableMetadata' order_smpl 'sampleMetadata' centering 'none'; fi] -ok -( w4mclassfilter ) > Test-2 ... 2021-03-11 20:12:47,331 INFO [galaxy.tools] Validated and populated state for tool request (18.574 ms) -2021-03-11 20:12:47,741 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 5 -2021-03-11 20:12:47,846 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=5,tool_id=upload1] (81.931 ms) -2021-03-11 20:12:47,846 INFO [galaxy.web_stack.handlers] (Job[id=5,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:12:47,870 INFO [galaxy.web_stack.handlers] (Job[id=5,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:12:48,122 INFO [galaxy.jobs.handler] (5) Job dispatched -2021-03-11 20:12:48,347 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/5/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/5/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/5/upload_params.json' '7:/tmp/tmp0krucrv3/job_working_directory/000/5/working/dataset_bf876626-ecef-4429-820a-c58971975308_files:/tmp/tmp0krucrv3/files/b/f/8/dataset_bf876626-ecef-4429-820a-c58971975308.dat'] -2021-03-11 20:12:53,344 INFO [galaxy.tools] Validated and populated state for tool request (25.298 ms) -2021-03-11 20:12:53,737 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 6 -2021-03-11 20:12:53,822 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=6,tool_id=upload1] (59.673 ms) -2021-03-11 20:12:53,822 INFO [galaxy.web_stack.handlers] (Job[id=6,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:12:53,832 INFO [galaxy.web_stack.handlers] (Job[id=6,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:12:54,598 INFO [galaxy.jobs.handler] (6) Job dispatched -2021-03-11 20:12:54,815 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/6/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/6/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/6/upload_params.json' '8:/tmp/tmp0krucrv3/job_working_directory/000/6/working/dataset_9125c62f-1424-44cd-825d-bd2192b5a7ae_files:/tmp/tmp0krucrv3/files/9/1/2/dataset_9125c62f-1424-44cd-825d-bd2192b5a7ae.dat'] -2021-03-11 20:12:59,663 INFO [galaxy.tools] Validated and populated state for tool request (17.604 ms) -2021-03-11 20:13:00,399 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 7 -2021-03-11 20:13:00,553 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=7,tool_id=upload1] (132.015 ms) -2021-03-11 20:13:00,553 INFO [galaxy.web_stack.handlers] (Job[id=7,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:00,561 INFO [galaxy.web_stack.handlers] (Job[id=7,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:01,216 INFO [galaxy.jobs.handler] (7) Job dispatched -2021-03-11 20:13:01,394 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/7/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/7/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/7/upload_params.json' '9:/tmp/tmp0krucrv3/job_working_directory/000/7/working/dataset_174e10fa-34b6-43ca-a220-7f9015586991_files:/tmp/tmp0krucrv3/files/1/7/4/dataset_174e10fa-34b6-43ca-a220-7f9015586991.dat'] -2021-03-11 20:13:06,451 INFO [galaxy.tools] Validated and populated state for tool request (29.066 ms) -2021-03-11 20:13:06,522 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool w4mclassfilter (0.863 ms) -2021-03-11 20:13:06,522 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool w4mclassfilter (0.561 ms) -2021-03-11 20:13:06,523 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool w4mclassfilter (0.598 ms) -2021-03-11 20:13:06,523 INFO [galaxy.tools.actions] Added output datasets to history (0.054 ms) -2021-03-11 20:13:06,525 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=w4mclassfilter] complete, ready to be enqueued (1.903 ms) -2021-03-11 20:13:06,728 INFO [galaxy.web_stack.handlers] (Job[id=8,tool_id=w4mclassfilter]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:07,666 INFO [galaxy.jobs.handler] (8) Job dispatched -2021-03-11 20:13:07,953 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/8/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; unset R_HOME; if [ 'none' == 'medoid' -a 'zero' == 'none' ]; then (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2); [ ! 1 ]; else Rscript /home/rstudio/.planemo/planemo_tmp_ahme9v2m/w4mclassfilter_wrapper.R dataMatrix_in '/tmp/tmp0krucrv3/files/b/f/8/dataset_bf876626-ecef-4429-820a-c58971975308.dat' sampleMetadata_in '/tmp/tmp0krucrv3/files/9/1/2/dataset_9125c62f-1424-44cd-825d-bd2192b5a7ae.dat' variableMetadata_in '/tmp/tmp0krucrv3/files/1/7/4/dataset_174e10fa-34b6-43ca-a220-7f9015586991.dat' sampleclassNames 'HU_[0-9][0-9][0-9]' inclusive 'TRUE' wildcards 'FALSE' classnameColumn 'sampleMetadata' samplenameColumn 'sampleMetadata' variable_range_filter 'FEATMAX:6.30103:,mz:200:,rt::800' transformation 'log10' imputation 'zero' dataMatrix_out '/tmp/tmp0krucrv3/files/4/e/b/dataset_4ebfd1d6-79d1-41a8-9634-5e7711f8f9ac.dat' sampleMetadata_out '/tmp/tmp0krucrv3/files/4/0/9/dataset_409a8bdd-1fb5-4d52-8698-2ce205b370e5.dat' variableMetadata_out '/tmp/tmp0krucrv3/files/2/8/9/dataset_2895c0e9-05a9-4b9b-a037-8c1e4ff59ff5.dat' order_vrbl 'variableMetadata' order_smpl 'sampleMetadata' centering 'none'; fi] -ok -( w4mclassfilter ) > Test-3 ... 2021-03-11 20:13:14,797 INFO [galaxy.tools] Validated and populated state for tool request (18.125 ms) -2021-03-11 20:13:15,738 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 9 -2021-03-11 20:13:15,881 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=9,tool_id=upload1] (121.748 ms) -2021-03-11 20:13:15,881 INFO [galaxy.web_stack.handlers] (Job[id=9,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:15,889 INFO [galaxy.web_stack.handlers] (Job[id=9,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:16,266 INFO [galaxy.jobs.handler] (9) Job dispatched -2021-03-11 20:13:16,562 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/9/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/9/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/9/upload_params.json' '13:/tmp/tmp0krucrv3/job_working_directory/000/9/working/dataset_8d0f2846-333f-46c2-a6c5-45109cd7df19_files:/tmp/tmp0krucrv3/files/8/d/0/dataset_8d0f2846-333f-46c2-a6c5-45109cd7df19.dat'] -2021-03-11 20:13:21,815 INFO [galaxy.tools] Validated and populated state for tool request (24.255 ms) -2021-03-11 20:13:22,296 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 10 -2021-03-11 20:13:22,385 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=10,tool_id=upload1] (65.708 ms) -2021-03-11 20:13:22,385 INFO [galaxy.web_stack.handlers] (Job[id=10,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:22,393 INFO [galaxy.web_stack.handlers] (Job[id=10,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:22,763 INFO [galaxy.jobs.handler] (10) Job dispatched -2021-03-11 20:13:23,011 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/10/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/10/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/10/upload_params.json' '14:/tmp/tmp0krucrv3/job_working_directory/000/10/working/dataset_070b5281-2739-4cb3-b5f5-9bbcfff88d9b_files:/tmp/tmp0krucrv3/files/0/7/0/dataset_070b5281-2739-4cb3-b5f5-9bbcfff88d9b.dat'] -2021-03-11 20:13:27,856 INFO [galaxy.tools] Validated and populated state for tool request (17.700 ms) -2021-03-11 20:13:28,341 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 11 -2021-03-11 20:13:28,422 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=11,tool_id=upload1] (52.774 ms) -2021-03-11 20:13:28,422 INFO [galaxy.web_stack.handlers] (Job[id=11,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:28,430 INFO [galaxy.web_stack.handlers] (Job[id=11,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:29,402 INFO [galaxy.jobs.handler] (11) Job dispatched -2021-03-11 20:13:29,569 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/11/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/11/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/11/upload_params.json' '15:/tmp/tmp0krucrv3/job_working_directory/000/11/working/dataset_c0c660b8-7f0e-47ea-99c6-13494f3e2081_files:/tmp/tmp0krucrv3/files/c/0/c/dataset_c0c660b8-7f0e-47ea-99c6-13494f3e2081.dat'] -2021-03-11 20:13:34,782 INFO [galaxy.tools] Validated and populated state for tool request (31.134 ms) -2021-03-11 20:13:34,858 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool w4mclassfilter (0.859 ms) -2021-03-11 20:13:34,859 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool w4mclassfilter (0.544 ms) -2021-03-11 20:13:34,860 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool w4mclassfilter (0.875 ms) -2021-03-11 20:13:34,860 INFO [galaxy.tools.actions] Added output datasets to history (0.054 ms) -2021-03-11 20:13:34,862 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=w4mclassfilter] complete, ready to be enqueued (1.957 ms) -2021-03-11 20:13:34,980 INFO [galaxy.web_stack.handlers] (Job[id=12,tool_id=w4mclassfilter]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:35,873 INFO [galaxy.jobs.handler] (12) Job dispatched -2021-03-11 20:13:36,153 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/12/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; unset R_HOME; if [ 'none' == 'medoid' -a 'zero' == 'none' ]; then (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2); [ ! 1 ]; else Rscript /home/rstudio/.planemo/planemo_tmp_ahme9v2m/w4mclassfilter_wrapper.R dataMatrix_in '/tmp/tmp0krucrv3/files/8/d/0/dataset_8d0f2846-333f-46c2-a6c5-45109cd7df19.dat' sampleMetadata_in '/tmp/tmp0krucrv3/files/0/7/0/dataset_070b5281-2739-4cb3-b5f5-9bbcfff88d9b.dat' variableMetadata_in '/tmp/tmp0krucrv3/files/c/0/c/dataset_c0c660b8-7f0e-47ea-99c6-13494f3e2081.dat' sampleclassNames 'M' inclusive 'TRUE' wildcards 'TRUE' classnameColumn 'gender' samplenameColumn 'sampleMetadata' variable_range_filter '' transformation 'none' imputation 'zero' dataMatrix_out '/tmp/tmp0krucrv3/files/f/c/8/dataset_fc8561d1-b75d-4100-b4ce-962299c8beb6.dat' sampleMetadata_out '/tmp/tmp0krucrv3/files/b/8/2/dataset_b8264a33-9369-436d-b271-4f5dba90a0e3.dat' variableMetadata_out '/tmp/tmp0krucrv3/files/0/e/4/dataset_0e419622-0880-415e-b3fe-0dd1c16d9275.dat' order_vrbl 'variableMetadata' order_smpl 'sampleMetadata' centering 'none'; fi] -ok -( w4mclassfilter ) > Test-4 ... 2021-03-11 20:13:42,704 INFO [galaxy.tools] Validated and populated state for tool request (19.348 ms) -2021-03-11 20:13:43,095 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 13 -2021-03-11 20:13:43,181 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=13,tool_id=upload1] (59.225 ms) -2021-03-11 20:13:43,182 INFO [galaxy.web_stack.handlers] (Job[id=13,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:43,190 INFO [galaxy.web_stack.handlers] (Job[id=13,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:43,566 INFO [galaxy.jobs.handler] (13) Job dispatched -2021-03-11 20:13:43,826 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/13/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/13/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/13/upload_params.json' '19:/tmp/tmp0krucrv3/job_working_directory/000/13/working/dataset_84bc78f7-1268-4dcf-b746-febd17d7317b_files:/tmp/tmp0krucrv3/files/8/4/b/dataset_84bc78f7-1268-4dcf-b746-febd17d7317b.dat'] -2021-03-11 20:13:48,667 INFO [galaxy.tools] Validated and populated state for tool request (23.579 ms) -2021-03-11 20:13:49,130 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 14 -2021-03-11 20:13:49,209 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=14,tool_id=upload1] (56.240 ms) -2021-03-11 20:13:49,209 INFO [galaxy.web_stack.handlers] (Job[id=14,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:49,217 INFO [galaxy.web_stack.handlers] (Job[id=14,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:50,602 INFO [galaxy.jobs.handler] (14) Job dispatched -2021-03-11 20:13:50,834 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/14/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/14/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/14/upload_params.json' '20:/tmp/tmp0krucrv3/job_working_directory/000/14/working/dataset_3651d875-060c-484f-a472-d04b918babc5_files:/tmp/tmp0krucrv3/files/3/6/5/dataset_3651d875-060c-484f-a472-d04b918babc5.dat'] -2021-03-11 20:13:56,096 INFO [galaxy.tools] Validated and populated state for tool request (18.085 ms) -2021-03-11 20:13:56,515 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 15 -2021-03-11 20:13:56,595 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=15,tool_id=upload1] (58.474 ms) -2021-03-11 20:13:56,596 INFO [galaxy.web_stack.handlers] (Job[id=15,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:56,604 INFO [galaxy.web_stack.handlers] (Job[id=15,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:13:57,068 INFO [galaxy.jobs.handler] (15) Job dispatched -2021-03-11 20:13:57,284 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/15/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/15/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/15/upload_params.json' '21:/tmp/tmp0krucrv3/job_working_directory/000/15/working/dataset_2c5ee32d-b467-4e48-b869-e9d48b917cb0_files:/tmp/tmp0krucrv3/files/2/c/5/dataset_2c5ee32d-b467-4e48-b869-e9d48b917cb0.dat'] -2021-03-11 20:14:02,144 INFO [galaxy.tools] Validated and populated state for tool request (23.669 ms) -2021-03-11 20:14:02,215 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool w4mclassfilter (0.919 ms) -2021-03-11 20:14:02,216 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool w4mclassfilter (0.582 ms) -2021-03-11 20:14:02,216 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool w4mclassfilter (0.542 ms) -2021-03-11 20:14:02,217 INFO [galaxy.tools.actions] Added output datasets to history (0.052 ms) -2021-03-11 20:14:02,221 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=w4mclassfilter] complete, ready to be enqueued (4.394 ms) -2021-03-11 20:14:02,431 INFO [galaxy.web_stack.handlers] (Job[id=16,tool_id=w4mclassfilter]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:14:03,768 INFO [galaxy.jobs.handler] (16) Job dispatched -2021-03-11 20:14:04,027 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/16/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; unset R_HOME; if [ 'none' == 'medoid' -a 'zero' == 'none' ]; then (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2); [ ! 1 ]; else Rscript /home/rstudio/.planemo/planemo_tmp_ahme9v2m/w4mclassfilter_wrapper.R dataMatrix_in '/tmp/tmp0krucrv3/files/8/4/b/dataset_84bc78f7-1268-4dcf-b746-febd17d7317b.dat' sampleMetadata_in '/tmp/tmp0krucrv3/files/3/6/5/dataset_3651d875-060c-484f-a472-d04b918babc5.dat' variableMetadata_in '/tmp/tmp0krucrv3/files/2/c/5/dataset_2c5ee32d-b467-4e48-b869-e9d48b917cb0.dat' sampleclassNames '*' inclusive 'TRUE' wildcards 'TRUE' classnameColumn 'gender' samplenameColumn 'sampleMetadata' variable_range_filter '' transformation 'none' imputation 'zero' dataMatrix_out '/tmp/tmp0krucrv3/files/e/d/3/dataset_ed370c46-de10-4469-a088-06a51f4fa500.dat' sampleMetadata_out '/tmp/tmp0krucrv3/files/e/f/3/dataset_ef35c50b-a6e4-4bd4-a593-438cdf7dc6c1.dat' variableMetadata_out '/tmp/tmp0krucrv3/files/f/7/e/dataset_f7ef0d66-1985-479d-a6bc-e6500447e461.dat' order_vrbl 'variableMetadata' order_smpl 'sampleMetadata' centering 'none'; fi] -ok -( w4mclassfilter ) > Test-5 ... 2021-03-11 20:14:10,473 INFO [galaxy.tools] Validated and populated state for tool request (18.062 ms) -2021-03-11 20:14:10,928 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 17 -2021-03-11 20:14:11,001 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=17,tool_id=upload1] (50.629 ms) -2021-03-11 20:14:11,001 INFO [galaxy.web_stack.handlers] (Job[id=17,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:14:11,013 INFO [galaxy.web_stack.handlers] (Job[id=17,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:14:11,319 INFO [galaxy.jobs.handler] (17) Job dispatched -2021-03-11 20:14:11,617 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/17/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/17/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/17/upload_params.json' '25:/tmp/tmp0krucrv3/job_working_directory/000/17/working/dataset_ffcc5f14-af57-4004-ae24-c839ea0b81aa_files:/tmp/tmp0krucrv3/files/f/f/c/dataset_ffcc5f14-af57-4004-ae24-c839ea0b81aa.dat'] -2021-03-11 20:14:16,862 INFO [galaxy.tools] Validated and populated state for tool request (18.956 ms) -2021-03-11 20:14:17,277 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 18 -2021-03-11 20:14:17,351 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=18,tool_id=upload1] (52.542 ms) -2021-03-11 20:14:17,352 INFO [galaxy.web_stack.handlers] (Job[id=18,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:14:17,359 INFO [galaxy.web_stack.handlers] (Job[id=18,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:14:18,007 INFO [galaxy.jobs.handler] (18) Job dispatched -2021-03-11 20:14:18,264 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/18/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/18/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/18/upload_params.json' '26:/tmp/tmp0krucrv3/job_working_directory/000/18/working/dataset_e44a8663-86d7-44b8-871d-67500b785d34_files:/tmp/tmp0krucrv3/files/e/4/4/dataset_e44a8663-86d7-44b8-871d-67500b785d34.dat'] -2021-03-11 20:14:23,178 INFO [galaxy.tools] Validated and populated state for tool request (19.653 ms) -2021-03-11 20:14:23,629 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 19 -2021-03-11 20:14:23,724 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=19,tool_id=upload1] (72.709 ms) -2021-03-11 20:14:23,724 INFO [galaxy.web_stack.handlers] (Job[id=19,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:14:23,733 INFO [galaxy.web_stack.handlers] (Job[id=19,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:14:24,709 INFO [galaxy.jobs.handler] (19) Job dispatched -2021-03-11 20:14:24,895 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/19/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/19/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/19/upload_params.json' '27:/tmp/tmp0krucrv3/job_working_directory/000/19/working/dataset_8d429121-091d-4d14-b869-efce1ff7b8ea_files:/tmp/tmp0krucrv3/files/8/d/4/dataset_8d429121-091d-4d14-b869-efce1ff7b8ea.dat'] -2021-03-11 20:14:30,148 INFO [galaxy.tools] Validated and populated state for tool request (23.781 ms) -2021-03-11 20:14:30,261 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool w4mclassfilter (0.869 ms) -2021-03-11 20:14:30,262 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool w4mclassfilter (0.552 ms) -2021-03-11 20:14:30,263 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool w4mclassfilter (0.584 ms) -2021-03-11 20:14:30,263 INFO [galaxy.tools.actions] Added output datasets to history (0.051 ms) -2021-03-11 20:14:30,265 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=w4mclassfilter] complete, ready to be enqueued (1.976 ms) -2021-03-11 20:14:30,472 INFO [galaxy.web_stack.handlers] (Job[id=20,tool_id=w4mclassfilter]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:14:31,176 INFO [galaxy.jobs.handler] (20) Job dispatched -2021-03-11 20:14:31,440 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/20/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; unset R_HOME; if [ 'none' == 'medoid' -a 'zero' == 'none' ]; then (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2); [ ! 1 ]; else Rscript /home/rstudio/.planemo/planemo_tmp_ahme9v2m/w4mclassfilter_wrapper.R dataMatrix_in '/tmp/tmp0krucrv3/files/f/f/c/dataset_ffcc5f14-af57-4004-ae24-c839ea0b81aa.dat' sampleMetadata_in '/tmp/tmp0krucrv3/files/e/4/4/dataset_e44a8663-86d7-44b8-871d-67500b785d34.dat' variableMetadata_in '/tmp/tmp0krucrv3/files/8/d/4/dataset_8d429121-091d-4d14-b869-efce1ff7b8ea.dat' sampleclassNames 'M' inclusive 'TRUE' wildcards 'FALSE' classnameColumn 'gender' samplenameColumn 'sampleMetadata' variable_range_filter '' transformation 'none' imputation 'zero' dataMatrix_out '/tmp/tmp0krucrv3/files/9/e/2/dataset_9e2415d2-3bc3-4c45-b472-e9e3ef4066cb.dat' sampleMetadata_out '/tmp/tmp0krucrv3/files/d/6/3/dataset_d63280b5-3cdb-467a-89c0-151f5cc8d645.dat' variableMetadata_out '/tmp/tmp0krucrv3/files/3/f/9/dataset_3f9a98ae-cf14-4322-bd8b-4f7c46d79c2e.dat' order_vrbl 'variableMetadata' order_smpl 'sampleMetadata' centering 'none'; fi] -ok -( w4mclassfilter ) > Test-6 ... 2021-03-11 20:14:37,916 INFO [galaxy.tools] Validated and populated state for tool request (18.012 ms) -2021-03-11 20:14:38,309 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 21 -2021-03-11 20:14:38,391 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=21,tool_id=upload1] (59.834 ms) -2021-03-11 20:14:38,391 INFO [galaxy.web_stack.handlers] (Job[id=21,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:14:38,401 INFO [galaxy.web_stack.handlers] (Job[id=21,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:14:38,763 INFO [galaxy.jobs.handler] (21) Job dispatched -2021-03-11 20:14:38,961 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/21/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/21/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/21/upload_params.json' '31:/tmp/tmp0krucrv3/job_working_directory/000/21/working/dataset_ca5da58c-6fc6-4fae-b657-0910c5fb87d0_files:/tmp/tmp0krucrv3/files/c/a/5/dataset_ca5da58c-6fc6-4fae-b657-0910c5fb87d0.dat'] -2021-03-11 20:14:44,111 INFO [galaxy.tools] Validated and populated state for tool request (18.402 ms) -2021-03-11 20:14:44,494 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 22 -2021-03-11 20:14:44,580 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=22,tool_id=upload1] (63.716 ms) -2021-03-11 20:14:44,580 INFO [galaxy.web_stack.handlers] (Job[id=22,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:14:44,587 INFO [galaxy.web_stack.handlers] (Job[id=22,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:14:45,505 INFO [galaxy.jobs.handler] (22) Job dispatched -2021-03-11 20:14:45,695 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/22/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/22/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/22/upload_params.json' '32:/tmp/tmp0krucrv3/job_working_directory/000/22/working/dataset_d7eec5b0-8126-4a42-a0df-e75eb6e64bf2_files:/tmp/tmp0krucrv3/files/d/7/e/dataset_d7eec5b0-8126-4a42-a0df-e75eb6e64bf2.dat'] -2021-03-11 20:14:50,803 INFO [galaxy.tools] Validated and populated state for tool request (17.668 ms) -2021-03-11 20:14:51,231 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 23 -2021-03-11 20:14:51,312 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=23,tool_id=upload1] (58.541 ms) -2021-03-11 20:14:51,312 INFO [galaxy.web_stack.handlers] (Job[id=23,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:14:51,320 INFO [galaxy.web_stack.handlers] (Job[id=23,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:14:52,043 INFO [galaxy.jobs.handler] (23) Job dispatched -2021-03-11 20:14:52,249 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/23/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/23/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/23/upload_params.json' '33:/tmp/tmp0krucrv3/job_working_directory/000/23/working/dataset_1eb2fe68-f352-4808-bda8-60ab5a51bd87_files:/tmp/tmp0krucrv3/files/1/e/b/dataset_1eb2fe68-f352-4808-bda8-60ab5a51bd87.dat'] -2021-03-11 20:14:57,192 INFO [galaxy.tools] Validated and populated state for tool request (23.383 ms) -2021-03-11 20:14:57,291 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool w4mclassfilter (0.883 ms) -2021-03-11 20:14:57,292 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool w4mclassfilter (0.701 ms) -2021-03-11 20:14:57,292 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool w4mclassfilter (0.541 ms) -2021-03-11 20:14:57,292 INFO [galaxy.tools.actions] Added output datasets to history (0.060 ms) -2021-03-11 20:14:57,294 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=w4mclassfilter] complete, ready to be enqueued (1.745 ms) -2021-03-11 20:14:57,476 INFO [galaxy.web_stack.handlers] (Job[id=24,tool_id=w4mclassfilter]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:14:58,530 INFO [galaxy.jobs.handler] (24) Job dispatched -2021-03-11 20:14:58,872 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/24/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; unset R_HOME; if [ 'none' == 'medoid' -a 'zero' == 'none' ]; then (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2); [ ! 1 ]; else Rscript /home/rstudio/.planemo/planemo_tmp_ahme9v2m/w4mclassfilter_wrapper.R dataMatrix_in '/tmp/tmp0krucrv3/files/c/a/5/dataset_ca5da58c-6fc6-4fae-b657-0910c5fb87d0.dat' sampleMetadata_in '/tmp/tmp0krucrv3/files/d/7/e/dataset_d7eec5b0-8126-4a42-a0df-e75eb6e64bf2.dat' variableMetadata_in '/tmp/tmp0krucrv3/files/1/e/b/dataset_1eb2fe68-f352-4808-bda8-60ab5a51bd87.dat' sampleclassNames 'M' inclusive 'TRUE' wildcards 'FALSE' classnameColumn 'gender' samplenameColumn 'sampleMetadata' variable_range_filter '' transformation 'none' imputation 'zero' dataMatrix_out '/tmp/tmp0krucrv3/files/2/a/3/dataset_2a3805e7-3619-441d-b271-4ca4b1fe0252.dat' sampleMetadata_out '/tmp/tmp0krucrv3/files/e/2/c/dataset_e2c62718-8cb4-409d-83d1-86bd4797080b.dat' variableMetadata_out '/tmp/tmp0krucrv3/files/d/1/b/dataset_d1b10903-1695-44d3-8c3b-f4b09f030258.dat' order_vrbl 'variableMetadata' order_smpl 'sampleMetadata' centering 'none'; fi] -ok -( w4mclassfilter ) > Test-7 ... 2021-03-11 20:15:05,471 INFO [galaxy.tools] Validated and populated state for tool request (18.880 ms) -2021-03-11 20:15:06,079 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 25 -2021-03-11 20:15:06,152 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=25,tool_id=upload1] (50.102 ms) -2021-03-11 20:15:06,152 INFO [galaxy.web_stack.handlers] (Job[id=25,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:15:06,161 INFO [galaxy.web_stack.handlers] (Job[id=25,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:15:07,308 INFO [galaxy.jobs.handler] (25) Job dispatched -2021-03-11 20:15:07,572 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/25/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/25/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/25/upload_params.json' '37:/tmp/tmp0krucrv3/job_working_directory/000/25/working/dataset_84a59741-f44e-4b5f-97db-8b98fc31981c_files:/tmp/tmp0krucrv3/files/8/4/a/dataset_84a59741-f44e-4b5f-97db-8b98fc31981c.dat'] -2021-03-11 20:15:12,798 INFO [galaxy.tools] Validated and populated state for tool request (23.031 ms) -2021-03-11 20:15:13,199 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 26 -2021-03-11 20:15:13,279 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=26,tool_id=upload1] (56.105 ms) -2021-03-11 20:15:13,279 INFO [galaxy.web_stack.handlers] (Job[id=26,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:15:13,287 INFO [galaxy.web_stack.handlers] (Job[id=26,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:15:13,795 INFO [galaxy.jobs.handler] (26) Job dispatched -2021-03-11 20:15:14,005 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/26/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/26/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/26/upload_params.json' '38:/tmp/tmp0krucrv3/job_working_directory/000/26/working/dataset_90af190f-2986-478e-b589-28a0b4e45db3_files:/tmp/tmp0krucrv3/files/9/0/a/dataset_90af190f-2986-478e-b589-28a0b4e45db3.dat'] -2021-03-11 20:15:18,974 INFO [galaxy.tools] Validated and populated state for tool request (41.847 ms) -2021-03-11 20:15:19,413 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 27 -2021-03-11 20:15:19,503 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=27,tool_id=upload1] (66.855 ms) -2021-03-11 20:15:19,503 INFO [galaxy.web_stack.handlers] (Job[id=27,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:15:19,512 INFO [galaxy.web_stack.handlers] (Job[id=27,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:15:20,566 INFO [galaxy.jobs.handler] (27) Job dispatched -2021-03-11 20:15:20,853 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/27/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/27/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/27/upload_params.json' '39:/tmp/tmp0krucrv3/job_working_directory/000/27/working/dataset_2ac2ab53-bba2-4ca1-be24-068d83216c3b_files:/tmp/tmp0krucrv3/files/2/a/c/dataset_2ac2ab53-bba2-4ca1-be24-068d83216c3b.dat'] -2021-03-11 20:15:26,117 INFO [galaxy.tools] Validated and populated state for tool request (23.522 ms) -2021-03-11 20:15:26,193 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool w4mclassfilter (0.887 ms) -2021-03-11 20:15:26,194 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool w4mclassfilter (0.560 ms) -2021-03-11 20:15:26,194 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool w4mclassfilter (0.559 ms) -2021-03-11 20:15:26,195 INFO [galaxy.tools.actions] Added output datasets to history (0.053 ms) -2021-03-11 20:15:26,197 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=w4mclassfilter] complete, ready to be enqueued (1.946 ms) -2021-03-11 20:15:26,329 INFO [galaxy.web_stack.handlers] (Job[id=28,tool_id=w4mclassfilter]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:15:27,076 INFO [galaxy.jobs.handler] (28) Job dispatched -2021-03-11 20:15:27,358 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/28/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; unset R_HOME; if [ 'none' == 'medoid' -a 'zero' == 'none' ]; then (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2); [ ! 1 ]; else Rscript /home/rstudio/.planemo/planemo_tmp_ahme9v2m/w4mclassfilter_wrapper.R dataMatrix_in '/tmp/tmp0krucrv3/files/8/4/a/dataset_84a59741-f44e-4b5f-97db-8b98fc31981c.dat' sampleMetadata_in '/tmp/tmp0krucrv3/files/9/0/a/dataset_90af190f-2986-478e-b589-28a0b4e45db3.dat' variableMetadata_in '/tmp/tmp0krucrv3/files/2/a/c/dataset_2ac2ab53-bba2-4ca1-be24-068d83216c3b.dat' sampleclassNames 'M' inclusive 'TRUE' wildcards 'FALSE' classnameColumn 'gender' samplenameColumn 'sampleMetadata' variable_range_filter '' transformation 'none' imputation 'zero' dataMatrix_out '/tmp/tmp0krucrv3/files/2/b/9/dataset_2b9977ea-cf31-48f3-8748-220a3bd81ae2.dat' sampleMetadata_out '/tmp/tmp0krucrv3/files/d/2/2/dataset_d222e264-f29d-4c0f-882a-c5b46caea2ae.dat' variableMetadata_out '/tmp/tmp0krucrv3/files/4/4/9/dataset_449c0e75-3a01-48b5-bc9c-9a42002a0cf1.dat' order_vrbl 'variableMetadata' order_smpl 'sampleMetadata' centering 'none'; fi] -ok -( w4mclassfilter ) > Test-8 ... 2021-03-11 20:15:33,564 INFO [galaxy.tools] Validated and populated state for tool request (17.705 ms) -2021-03-11 20:15:34,005 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 29 -2021-03-11 20:15:34,137 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=29,tool_id=upload1] (111.244 ms) -2021-03-11 20:15:34,138 INFO [galaxy.web_stack.handlers] (Job[id=29,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:15:34,146 INFO [galaxy.web_stack.handlers] (Job[id=29,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:15:34,683 INFO [galaxy.jobs.handler] (29) Job dispatched -2021-03-11 20:15:34,985 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/29/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/29/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/29/upload_params.json' '43:/tmp/tmp0krucrv3/job_working_directory/000/29/working/dataset_3825439a-e350-43c0-88cd-4f2ceb698f9b_files:/tmp/tmp0krucrv3/files/3/8/2/dataset_3825439a-e350-43c0-88cd-4f2ceb698f9b.dat'] -2021-03-11 20:15:40,163 INFO [galaxy.tools] Validated and populated state for tool request (22.321 ms) -2021-03-11 20:15:40,923 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 30 -2021-03-11 20:15:41,030 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=30,tool_id=upload1] (76.558 ms) -2021-03-11 20:15:41,030 INFO [galaxy.web_stack.handlers] (Job[id=30,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:15:41,038 INFO [galaxy.web_stack.handlers] (Job[id=30,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:15:42,204 INFO [galaxy.jobs.handler] (30) Job dispatched -2021-03-11 20:15:42,408 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/30/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/30/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/30/upload_params.json' '44:/tmp/tmp0krucrv3/job_working_directory/000/30/working/dataset_5b5bd9ea-15e4-4b0d-9b8b-ed71505cf953_files:/tmp/tmp0krucrv3/files/5/b/5/dataset_5b5bd9ea-15e4-4b0d-9b8b-ed71505cf953.dat'] -2021-03-11 20:15:47,425 INFO [galaxy.tools] Validated and populated state for tool request (42.876 ms) -2021-03-11 20:15:47,875 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 31 -2021-03-11 20:15:47,954 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=31,tool_id=upload1] (56.574 ms) -2021-03-11 20:15:47,954 INFO [galaxy.web_stack.handlers] (Job[id=31,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:15:47,962 INFO [galaxy.web_stack.handlers] (Job[id=31,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:15:48,676 INFO [galaxy.jobs.handler] (31) Job dispatched -2021-03-11 20:15:48,923 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/31/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/31/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/31/upload_params.json' '45:/tmp/tmp0krucrv3/job_working_directory/000/31/working/dataset_8333b8bd-f93b-4520-a0cb-9bb802d3ab75_files:/tmp/tmp0krucrv3/files/8/3/3/dataset_8333b8bd-f93b-4520-a0cb-9bb802d3ab75.dat'] -2021-03-11 20:15:54,006 INFO [galaxy.tools] Validated and populated state for tool request (21.360 ms) -2021-03-11 20:15:54,082 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool w4mclassfilter (0.813 ms) -2021-03-11 20:15:54,083 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool w4mclassfilter (0.593 ms) -2021-03-11 20:15:54,084 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool w4mclassfilter (0.540 ms) -2021-03-11 20:15:54,084 INFO [galaxy.tools.actions] Added output datasets to history (0.051 ms) -2021-03-11 20:15:54,088 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=w4mclassfilter] complete, ready to be enqueued (3.968 ms) -2021-03-11 20:15:54,217 INFO [galaxy.web_stack.handlers] (Job[id=32,tool_id=w4mclassfilter]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:15:55,707 INFO [galaxy.jobs.handler] (32) Job dispatched -2021-03-11 20:15:56,067 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/32/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; unset R_HOME; if [ 'none' == 'medoid' -a 'zero' == 'none' ]; then (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2); [ ! 1 ]; else Rscript /home/rstudio/.planemo/planemo_tmp_ahme9v2m/w4mclassfilter_wrapper.R dataMatrix_in '/tmp/tmp0krucrv3/files/3/8/2/dataset_3825439a-e350-43c0-88cd-4f2ceb698f9b.dat' sampleMetadata_in '/tmp/tmp0krucrv3/files/5/b/5/dataset_5b5bd9ea-15e4-4b0d-9b8b-ed71505cf953.dat' variableMetadata_in '/tmp/tmp0krucrv3/files/8/3/3/dataset_8333b8bd-f93b-4520-a0cb-9bb802d3ab75.dat' sampleclassNames '[Mm],[fF]' inclusive 'TRUE' wildcards 'FALSE' classnameColumn 'gender' samplenameColumn 'sampleMetadata' variable_range_filter '' transformation 'none' imputation 'zero' dataMatrix_out '/tmp/tmp0krucrv3/files/7/e/3/dataset_7e3d31f2-92c6-4b21-bf6b-e68ba451b5cb.dat' sampleMetadata_out '/tmp/tmp0krucrv3/files/c/4/7/dataset_c478b4cb-b6df-405f-8217-48654a1dca74.dat' variableMetadata_out '/tmp/tmp0krucrv3/files/9/a/c/dataset_9ac5e33f-f45f-4f72-a01f-ce3de1402411.dat' order_vrbl 'variableMetadata' order_smpl 'sampleMetadata' centering 'none'; fi] -ok -( w4mclassfilter ) > Test-9 ... 2021-03-11 20:16:02,438 INFO [galaxy.tools] Validated and populated state for tool request (20.871 ms) -2021-03-11 20:16:02,887 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 33 -2021-03-11 20:16:03,008 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=33,tool_id=upload1] (99.006 ms) -2021-03-11 20:16:03,008 INFO [galaxy.web_stack.handlers] (Job[id=33,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:03,016 INFO [galaxy.web_stack.handlers] (Job[id=33,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:03,351 INFO [galaxy.jobs.handler] (33) Job dispatched -2021-03-11 20:16:03,522 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/33/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/33/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/33/upload_params.json' '49:/tmp/tmp0krucrv3/job_working_directory/000/33/working/dataset_c565d33f-2981-4784-bf4a-1c2967fbed8c_files:/tmp/tmp0krucrv3/files/c/5/6/dataset_c565d33f-2981-4784-bf4a-1c2967fbed8c.dat'] -2021-03-11 20:16:08,725 INFO [galaxy.tools] Validated and populated state for tool request (23.735 ms) -2021-03-11 20:16:09,150 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 34 -2021-03-11 20:16:09,229 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=34,tool_id=upload1] (56.778 ms) -2021-03-11 20:16:09,229 INFO [galaxy.web_stack.handlers] (Job[id=34,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:09,237 INFO [galaxy.web_stack.handlers] (Job[id=34,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:09,820 INFO [galaxy.jobs.handler] (34) Job dispatched -2021-03-11 20:16:10,018 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/34/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/34/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/34/upload_params.json' '50:/tmp/tmp0krucrv3/job_working_directory/000/34/working/dataset_3eb9049a-14d6-4b99-812e-a39abcc98b28_files:/tmp/tmp0krucrv3/files/3/e/b/dataset_3eb9049a-14d6-4b99-812e-a39abcc98b28.dat'] -2021-03-11 20:16:15,068 INFO [galaxy.tools] Validated and populated state for tool request (24.349 ms) -2021-03-11 20:16:16,007 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 35 -2021-03-11 20:16:16,086 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=35,tool_id=upload1] (57.948 ms) -2021-03-11 20:16:16,087 INFO [galaxy.web_stack.handlers] (Job[id=35,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:16,105 INFO [galaxy.web_stack.handlers] (Job[id=35,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:16,443 INFO [galaxy.jobs.handler] (35) Job dispatched -2021-03-11 20:16:16,750 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/35/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/35/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/35/upload_params.json' '51:/tmp/tmp0krucrv3/job_working_directory/000/35/working/dataset_6e18a0f1-211d-4e0d-8170-809dd3566b3b_files:/tmp/tmp0krucrv3/files/6/e/1/dataset_6e18a0f1-211d-4e0d-8170-809dd3566b3b.dat'] -2021-03-11 20:16:22,180 INFO [galaxy.tools] Validated and populated state for tool request (21.444 ms) -2021-03-11 20:16:22,270 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool w4mclassfilter (0.875 ms) -2021-03-11 20:16:22,270 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool w4mclassfilter (0.555 ms) -2021-03-11 20:16:22,271 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool w4mclassfilter (0.818 ms) -2021-03-11 20:16:22,272 INFO [galaxy.tools.actions] Added output datasets to history (0.053 ms) -2021-03-11 20:16:22,274 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=w4mclassfilter] complete, ready to be enqueued (1.941 ms) -2021-03-11 20:16:22,442 INFO [galaxy.web_stack.handlers] (Job[id=36,tool_id=w4mclassfilter]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:23,170 INFO [galaxy.jobs.handler] (36) Job dispatched -2021-03-11 20:16:23,421 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/36/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; unset R_HOME; if [ 'none' == 'medoid' -a 'zero' == 'none' ]; then (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2); [ ! 1 ]; else Rscript /home/rstudio/.planemo/planemo_tmp_ahme9v2m/w4mclassfilter_wrapper.R dataMatrix_in '/tmp/tmp0krucrv3/files/c/5/6/dataset_c565d33f-2981-4784-bf4a-1c2967fbed8c.dat' sampleMetadata_in '/tmp/tmp0krucrv3/files/3/e/b/dataset_3eb9049a-14d6-4b99-812e-a39abcc98b28.dat' variableMetadata_in '/tmp/tmp0krucrv3/files/6/e/1/dataset_6e18a0f1-211d-4e0d-8170-809dd3566b3b.dat' sampleclassNames 'M' inclusive 'TRUE' wildcards 'FALSE' classnameColumn '' samplenameColumn 'sampleMetadata' variable_range_filter '' transformation 'none' imputation 'zero' dataMatrix_out '/tmp/tmp0krucrv3/files/1/f/9/dataset_1f9df5e3-4034-47be-86fd-1505f87bd782.dat' sampleMetadata_out '/tmp/tmp0krucrv3/files/3/5/a/dataset_35a5842e-5652-4de8-8652-e837af324847.dat' variableMetadata_out '/tmp/tmp0krucrv3/files/9/9/c/dataset_99c48f69-2e27-49ec-a904-04800f2aa0c5.dat' order_vrbl 'variableMetadata' order_smpl 'sampleMetadata' centering 'none'; fi] -ok -( w4mclassfilter ) > Test-10 ... 2021-03-11 20:16:29,808 INFO [galaxy.tools] Validated and populated state for tool request (20.731 ms) -2021-03-11 20:16:30,597 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 37 -2021-03-11 20:16:30,727 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=37,tool_id=upload1] (92.441 ms) -2021-03-11 20:16:30,727 INFO [galaxy.web_stack.handlers] (Job[id=37,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:30,735 INFO [galaxy.web_stack.handlers] (Job[id=37,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:31,894 INFO [galaxy.jobs.handler] (37) Job dispatched -2021-03-11 20:16:32,112 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/37/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/37/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/37/upload_params.json' '55:/tmp/tmp0krucrv3/job_working_directory/000/37/working/dataset_fc0f9b8e-b6e7-4017-b7cf-59b48a5af20d_files:/tmp/tmp0krucrv3/files/f/c/0/dataset_fc0f9b8e-b6e7-4017-b7cf-59b48a5af20d.dat'] -2021-03-11 20:16:37,181 INFO [galaxy.tools] Validated and populated state for tool request (23.289 ms) -2021-03-11 20:16:37,620 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 38 -2021-03-11 20:16:37,717 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=38,tool_id=upload1] (70.015 ms) -2021-03-11 20:16:37,717 INFO [galaxy.web_stack.handlers] (Job[id=38,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:37,726 INFO [galaxy.web_stack.handlers] (Job[id=38,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:38,387 INFO [galaxy.jobs.handler] (38) Job dispatched -2021-03-11 20:16:38,666 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/38/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/38/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/38/upload_params.json' '56:/tmp/tmp0krucrv3/job_working_directory/000/38/working/dataset_7f14d0a0-c31c-4d8d-a380-b08a246037ac_files:/tmp/tmp0krucrv3/files/7/f/1/dataset_7f14d0a0-c31c-4d8d-a380-b08a246037ac.dat'] -2021-03-11 20:16:43,561 INFO [galaxy.tools] Validated and populated state for tool request (18.436 ms) -2021-03-11 20:16:44,049 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 39 -2021-03-11 20:16:44,173 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=39,tool_id=upload1] (102.656 ms) -2021-03-11 20:16:44,174 INFO [galaxy.web_stack.handlers] (Job[id=39,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:44,182 INFO [galaxy.web_stack.handlers] (Job[id=39,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:45,070 INFO [galaxy.jobs.handler] (39) Job dispatched -2021-03-11 20:16:45,437 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/39/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/39/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/39/upload_params.json' '57:/tmp/tmp0krucrv3/job_working_directory/000/39/working/dataset_f0aaad10-f102-45f3-98fc-bfb82e15e313_files:/tmp/tmp0krucrv3/files/f/0/a/dataset_f0aaad10-f102-45f3-98fc-bfb82e15e313.dat'] -2021-03-11 20:16:50,618 INFO [galaxy.tools] Validated and populated state for tool request (23.031 ms) -2021-03-11 20:16:50,691 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool w4mclassfilter (0.940 ms) -2021-03-11 20:16:50,692 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool w4mclassfilter (0.532 ms) -2021-03-11 20:16:50,693 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool w4mclassfilter (0.526 ms) -2021-03-11 20:16:50,693 INFO [galaxy.tools.actions] Added output datasets to history (0.051 ms) -2021-03-11 20:16:50,695 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=w4mclassfilter] complete, ready to be enqueued (1.875 ms) -2021-03-11 20:16:50,828 INFO [galaxy.web_stack.handlers] (Job[id=40,tool_id=w4mclassfilter]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:51,836 INFO [galaxy.jobs.handler] (40) Job dispatched -2021-03-11 20:16:52,124 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/40/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; unset R_HOME; if [ 'none' == 'medoid' -a 'none' == 'none' ]; then (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2); [ ! 1 ]; else Rscript /home/rstudio/.planemo/planemo_tmp_ahme9v2m/w4mclassfilter_wrapper.R dataMatrix_in '/tmp/tmp0krucrv3/files/f/c/0/dataset_fc0f9b8e-b6e7-4017-b7cf-59b48a5af20d.dat' sampleMetadata_in '/tmp/tmp0krucrv3/files/7/f/1/dataset_7f14d0a0-c31c-4d8d-a380-b08a246037ac.dat' variableMetadata_in '/tmp/tmp0krucrv3/files/f/0/a/dataset_f0aaad10-f102-45f3-98fc-bfb82e15e313.dat' sampleclassNames '*' inclusive 'TRUE' wildcards 'TRUE' classnameColumn 'gender' samplenameColumn 'sampleMetadata' variable_range_filter '' transformation 'none' imputation 'none' dataMatrix_out '/tmp/tmp0krucrv3/files/4/d/a/dataset_4dac97ff-daa7-4232-aedb-1cd3233b1814.dat' sampleMetadata_out '/tmp/tmp0krucrv3/files/b/f/1/dataset_bf1700a9-d01e-422e-9e55-546e70f56d49.dat' variableMetadata_out '/tmp/tmp0krucrv3/files/b/8/1/dataset_b819f292-3ec8-49e0-98d0-0b1da99b3294.dat' order_vrbl 'variableMetadata' order_smpl 'sampleMetadata' centering 'none'; fi] -ok -( w4mclassfilter ) > Test-11 ... 2021-03-11 20:16:58,561 INFO [galaxy.tools] Validated and populated state for tool request (19.145 ms) -2021-03-11 20:16:59,028 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 41 -2021-03-11 20:16:59,137 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=41,tool_id=upload1] (87.674 ms) -2021-03-11 20:16:59,138 INFO [galaxy.web_stack.handlers] (Job[id=41,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:59,146 INFO [galaxy.web_stack.handlers] (Job[id=41,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:16:59,579 INFO [galaxy.jobs.handler] (41) Job dispatched -2021-03-11 20:16:59,805 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/41/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/41/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/41/upload_params.json' '61:/tmp/tmp0krucrv3/job_working_directory/000/41/working/dataset_e1acbbbf-9514-4893-bb09-2336c5ae0f3a_files:/tmp/tmp0krucrv3/files/e/1/a/dataset_e1acbbbf-9514-4893-bb09-2336c5ae0f3a.dat'] -2021-03-11 20:17:05,043 INFO [galaxy.tools] Validated and populated state for tool request (24.592 ms) -2021-03-11 20:17:06,102 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 42 -2021-03-11 20:17:06,231 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=42,tool_id=upload1] (100.617 ms) -2021-03-11 20:17:06,231 INFO [galaxy.web_stack.handlers] (Job[id=42,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:17:06,239 INFO [galaxy.web_stack.handlers] (Job[id=42,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:17:07,241 INFO [galaxy.jobs.handler] (42) Job dispatched -2021-03-11 20:17:07,411 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/42/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/42/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/42/upload_params.json' '62:/tmp/tmp0krucrv3/job_working_directory/000/42/working/dataset_6246ec07-2ddc-4660-b975-99775fa5e1a6_files:/tmp/tmp0krucrv3/files/6/2/4/dataset_6246ec07-2ddc-4660-b975-99775fa5e1a6.dat'] -2021-03-11 20:17:12,542 INFO [galaxy.tools] Validated and populated state for tool request (17.874 ms) -2021-03-11 20:17:12,933 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 43 -2021-03-11 20:17:13,022 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=43,tool_id=upload1] (67.071 ms) -2021-03-11 20:17:13,024 INFO [galaxy.web_stack.handlers] (Job[id=43,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:17:13,034 INFO [galaxy.web_stack.handlers] (Job[id=43,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:17:13,728 INFO [galaxy.jobs.handler] (43) Job dispatched -2021-03-11 20:17:13,962 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/43/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/43/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/43/upload_params.json' '63:/tmp/tmp0krucrv3/job_working_directory/000/43/working/dataset_0423f1ea-b226-49c6-8f07-41111d98d928_files:/tmp/tmp0krucrv3/files/0/4/2/dataset_0423f1ea-b226-49c6-8f07-41111d98d928.dat'] -2021-03-11 20:17:19,025 INFO [galaxy.tools] Validated and populated state for tool request (21.754 ms) -2021-03-11 20:17:19,117 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool w4mclassfilter (0.942 ms) -2021-03-11 20:17:19,118 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool w4mclassfilter (0.560 ms) -2021-03-11 20:17:19,119 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool w4mclassfilter (0.541 ms) -2021-03-11 20:17:19,119 INFO [galaxy.tools.actions] Added output datasets to history (0.051 ms) -2021-03-11 20:17:19,121 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=w4mclassfilter] complete, ready to be enqueued (1.911 ms) -2021-03-11 20:17:19,315 INFO [galaxy.web_stack.handlers] (Job[id=44,tool_id=w4mclassfilter]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:17:20,452 INFO [galaxy.jobs.handler] (44) Job dispatched -2021-03-11 20:17:20,732 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/44/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; unset R_HOME; if [ 'none' == 'medoid' -a 'center' == 'none' ]; then (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2); [ ! 1 ]; else Rscript /home/rstudio/.planemo/planemo_tmp_ahme9v2m/w4mclassfilter_wrapper.R dataMatrix_in '/tmp/tmp0krucrv3/files/e/1/a/dataset_e1acbbbf-9514-4893-bb09-2336c5ae0f3a.dat' sampleMetadata_in '/tmp/tmp0krucrv3/files/6/2/4/dataset_6246ec07-2ddc-4660-b975-99775fa5e1a6.dat' variableMetadata_in '/tmp/tmp0krucrv3/files/0/4/2/dataset_0423f1ea-b226-49c6-8f07-41111d98d928.dat' sampleclassNames '*' inclusive 'TRUE' wildcards 'TRUE' classnameColumn 'gender' samplenameColumn 'sampleMetadata' variable_range_filter '' transformation 'none' imputation 'center' dataMatrix_out '/tmp/tmp0krucrv3/files/d/0/6/dataset_d061ceaa-ed95-47e7-9ef5-4c3aeccf7d9d.dat' sampleMetadata_out '/tmp/tmp0krucrv3/files/1/0/b/dataset_10b443a1-6fac-4c5c-a6f5-6f6f8a43dd6a.dat' variableMetadata_out '/tmp/tmp0krucrv3/files/d/9/9/dataset_d99c8d72-c5ff-423d-b580-1722082a0da5.dat' order_vrbl 'variableMetadata' order_smpl 'sampleMetadata' centering 'none'; fi] -ok -( w4mclassfilter ) > Test-12 ... 2021-03-11 20:17:27,322 INFO [galaxy.tools] Validated and populated state for tool request (24.887 ms) -2021-03-11 20:17:27,769 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 45 -2021-03-11 20:17:27,859 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=45,tool_id=upload1] (60.698 ms) -2021-03-11 20:17:27,859 INFO [galaxy.web_stack.handlers] (Job[id=45,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:17:27,867 INFO [galaxy.web_stack.handlers] (Job[id=45,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:17:29,040 INFO [galaxy.jobs.handler] (45) Job dispatched -2021-03-11 20:17:29,371 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/45/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/45/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/45/upload_params.json' '67:/tmp/tmp0krucrv3/job_working_directory/000/45/working/dataset_fec32c80-a50c-40c5-9ac7-7eb3f548e0ec_files:/tmp/tmp0krucrv3/files/f/e/c/dataset_fec32c80-a50c-40c5-9ac7-7eb3f548e0ec.dat'] -2021-03-11 20:17:34,444 INFO [galaxy.tools] Validated and populated state for tool request (22.764 ms) -2021-03-11 20:17:34,827 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 46 -2021-03-11 20:17:34,917 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=46,tool_id=upload1] (68.770 ms) -2021-03-11 20:17:34,917 INFO [galaxy.web_stack.handlers] (Job[id=46,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:17:34,927 INFO [galaxy.web_stack.handlers] (Job[id=46,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:17:35,585 INFO [galaxy.jobs.handler] (46) Job dispatched -2021-03-11 20:17:35,833 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/46/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/46/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/46/upload_params.json' '68:/tmp/tmp0krucrv3/job_working_directory/000/46/working/dataset_9c9475ac-b54e-457f-97cc-8aa303356f1c_files:/tmp/tmp0krucrv3/files/9/c/9/dataset_9c9475ac-b54e-457f-97cc-8aa303356f1c.dat'] -2021-03-11 20:17:40,882 INFO [galaxy.tools] Validated and populated state for tool request (31.460 ms) -2021-03-11 20:17:41,296 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 47 -2021-03-11 20:17:41,380 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=47,tool_id=upload1] (62.340 ms) -2021-03-11 20:17:41,380 INFO [galaxy.web_stack.handlers] (Job[id=47,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:17:41,388 INFO [galaxy.web_stack.handlers] (Job[id=47,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:17:42,232 INFO [galaxy.jobs.handler] (47) Job dispatched -2021-03-11 20:17:42,484 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/47/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/47/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/47/upload_params.json' '69:/tmp/tmp0krucrv3/job_working_directory/000/47/working/dataset_5d5a49c3-2db3-4439-b7dc-31f6d2a60688_files:/tmp/tmp0krucrv3/files/5/d/5/dataset_5d5a49c3-2db3-4439-b7dc-31f6d2a60688.dat'] -2021-03-11 20:17:47,475 INFO [galaxy.tools] Validated and populated state for tool request (39.634 ms) -2021-03-11 20:17:47,551 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool w4mclassfilter (0.875 ms) -2021-03-11 20:17:47,552 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool w4mclassfilter (0.560 ms) -2021-03-11 20:17:47,553 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool w4mclassfilter (0.542 ms) -2021-03-11 20:17:47,553 INFO [galaxy.tools.actions] Added output datasets to history (0.057 ms) -2021-03-11 20:17:47,555 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=w4mclassfilter] complete, ready to be enqueued (1.873 ms) -2021-03-11 20:17:47,689 INFO [galaxy.web_stack.handlers] (Job[id=48,tool_id=w4mclassfilter]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:17:48,786 INFO [galaxy.jobs.handler] (48) Job dispatched -2021-03-11 20:17:49,084 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/48/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; unset R_HOME; if [ 'medoid' == 'medoid' -a 'zero' == 'none' ]; then (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2); [ ! 1 ]; else Rscript /home/rstudio/.planemo/planemo_tmp_ahme9v2m/w4mclassfilter_wrapper.R dataMatrix_in '/tmp/tmp0krucrv3/files/f/e/c/dataset_fec32c80-a50c-40c5-9ac7-7eb3f548e0ec.dat' sampleMetadata_in '/tmp/tmp0krucrv3/files/9/c/9/dataset_9c9475ac-b54e-457f-97cc-8aa303356f1c.dat' variableMetadata_in '/tmp/tmp0krucrv3/files/5/d/5/dataset_5d5a49c3-2db3-4439-b7dc-31f6d2a60688.dat' sampleclassNames '' inclusive 'FALSE' wildcards 'TRUE' classnameColumn 'gender' samplenameColumn 'sampleMetadata' variable_range_filter '' transformation 'none' imputation 'zero' dataMatrix_out '/tmp/tmp0krucrv3/files/9/e/c/dataset_9ec12057-e344-45c5-948e-b49a88882954.dat' sampleMetadata_out '/tmp/tmp0krucrv3/files/7/9/5/dataset_795e4bcb-007c-4b55-b116-8ba1d6f290cd.dat' variableMetadata_out '/tmp/tmp0krucrv3/files/9/6/a/dataset_96addb90-7248-4340-87be-bbd769b3aaba.dat' order_vrbl 'rt' order_smpl 'gender' centering 'medoid'; fi] -ok -( w4mclassfilter ) > Test-13 ... 2021-03-11 20:17:55,544 INFO [galaxy.tools] Validated and populated state for tool request (18.023 ms) -2021-03-11 20:17:56,086 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 49 -2021-03-11 20:17:56,209 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=49,tool_id=upload1] (96.246 ms) -2021-03-11 20:17:56,209 INFO [galaxy.web_stack.handlers] (Job[id=49,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:17:56,221 INFO [galaxy.web_stack.handlers] (Job[id=49,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:17:56,463 INFO [galaxy.jobs.handler] (49) Job dispatched -2021-03-11 20:17:56,689 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/49/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/49/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/49/upload_params.json' '73:/tmp/tmp0krucrv3/job_working_directory/000/49/working/dataset_deb04e85-d7f8-481d-b03c-5189ce9b2a9f_files:/tmp/tmp0krucrv3/files/d/e/b/dataset_deb04e85-d7f8-481d-b03c-5189ce9b2a9f.dat'] -2021-03-11 20:18:01,857 INFO [galaxy.tools] Validated and populated state for tool request (18.320 ms) -2021-03-11 20:18:02,343 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 50 -2021-03-11 20:18:02,439 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=50,tool_id=upload1] (73.807 ms) -2021-03-11 20:18:02,439 INFO [galaxy.web_stack.handlers] (Job[id=50,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:18:02,447 INFO [galaxy.web_stack.handlers] (Job[id=50,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:18:02,896 INFO [galaxy.jobs.handler] (50) Job dispatched -2021-03-11 20:18:03,096 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/50/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/50/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/50/upload_params.json' '74:/tmp/tmp0krucrv3/job_working_directory/000/50/working/dataset_c772a3d6-a6ef-49e0-a8f7-d3dc057cdba4_files:/tmp/tmp0krucrv3/files/c/7/7/dataset_c772a3d6-a6ef-49e0-a8f7-d3dc057cdba4.dat'] -2021-03-11 20:18:08,117 INFO [galaxy.tools] Validated and populated state for tool request (18.717 ms) -2021-03-11 20:18:08,617 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 51 -2021-03-11 20:18:08,811 INFO [galaxy.web_stack.handlers] Flushed transaction for Job[id=51,tool_id=upload1] (172.238 ms) -2021-03-11 20:18:08,811 INFO [galaxy.web_stack.handlers] (Job[id=51,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:18:08,819 INFO [galaxy.web_stack.handlers] (Job[id=51,tool_id=upload1]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:18:09,485 INFO [galaxy.jobs.handler] (51) Job dispatched -2021-03-11 20:18:09,720 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/51/tool_script.sh] for tool command [python '/tmp/tmp0krucrv3/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp0krucrv3/galaxy-dev' '/tmp/tmp0krucrv3/job_working_directory/000/51/registry.xml' '/tmp/tmp0krucrv3/job_working_directory/000/51/upload_params.json' '75:/tmp/tmp0krucrv3/job_working_directory/000/51/working/dataset_afad8efa-19e8-47e7-a6bd-6d55e0539a44_files:/tmp/tmp0krucrv3/files/a/f/a/dataset_afad8efa-19e8-47e7-a6bd-6d55e0539a44.dat'] -2021-03-11 20:18:15,145 INFO [galaxy.tools] Validated and populated state for tool request (24.130 ms) -2021-03-11 20:18:15,222 INFO [galaxy.tools.actions] Handled output named dataMatrix_out for tool w4mclassfilter (0.879 ms) -2021-03-11 20:18:15,223 INFO [galaxy.tools.actions] Handled output named sampleMetadata_out for tool w4mclassfilter (0.585 ms) -2021-03-11 20:18:15,224 INFO [galaxy.tools.actions] Handled output named variableMetadata_out for tool w4mclassfilter (0.565 ms) -2021-03-11 20:18:15,224 INFO [galaxy.tools.actions] Added output datasets to history (0.052 ms) -2021-03-11 20:18:15,226 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=w4mclassfilter] complete, ready to be enqueued (1.970 ms) -2021-03-11 20:18:15,573 INFO [galaxy.web_stack.handlers] (Job[id=52,tool_id=w4mclassfilter]) Handler 'main' assigned using 'db-preassign' assignment method -2021-03-11 20:18:16,041 INFO [galaxy.jobs.handler] (52) Job dispatched -2021-03-11 20:18:16,357 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp0krucrv3/job_working_directory/000/52/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/rstudio/miniconda3/bin/activate' '/home/rstudio/miniconda3/envs/mulled-v1-132b61d9c88900ff975b44a9aad2b439393214f7dc447ec92cf134b55ae57521' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; unset R_HOME; if [ 'medoid' == 'medoid' -a 'zero' == 'none' ]; then (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2); [ ! 1 ]; else Rscript /home/rstudio/.planemo/planemo_tmp_ahme9v2m/w4mclassfilter_wrapper.R dataMatrix_in '/tmp/tmp0krucrv3/files/d/e/b/dataset_deb04e85-d7f8-481d-b03c-5189ce9b2a9f.dat' sampleMetadata_in '/tmp/tmp0krucrv3/files/c/7/7/dataset_c772a3d6-a6ef-49e0-a8f7-d3dc057cdba4.dat' variableMetadata_in '/tmp/tmp0krucrv3/files/a/f/a/dataset_afad8efa-19e8-47e7-a6bd-6d55e0539a44.dat' sampleclassNames '' inclusive 'FALSE' wildcards 'TRUE' classnameColumn 'pcgroup' samplenameColumn 'sampleMetadata' variable_range_filter '' transformation 'none' imputation 'zero' dataMatrix_out '/tmp/tmp0krucrv3/files/7/1/1/dataset_711ba603-0791-41a7-ac7d-6bc401054381.dat' sampleMetadata_out '/tmp/tmp0krucrv3/files/e/7/3/dataset_e73aa99b-e412-4c7f-acd6-808e6f83e083.dat' variableMetadata_out '/tmp/tmp0krucrv3/files/d/b/f/dataset_dbf8bc47-81f4-4c87-8511-0bc876a46927.dat' order_vrbl 'sample' order_smpl 'pcgroup' centering 'medoid'; fi] -ok - ----------------------------------------------------------------------- -XML: /tmp/tmp0krucrv3/xunit.xml ----------------------------------------------------------------------- -Ran 13 tests in 363.871s - -OK -2021-03-11 20:18:22,641 INFO [test_driver] Shutting down -2021-03-11 20:18:22,642 INFO [test_driver] Shutting down embedded galaxy web server -2021-03-11 20:18:22,644 INFO [test_driver] Embedded web server galaxy stopped -2021-03-11 20:18:22,644 INFO [test_driver] Stopping application galaxy -2021-03-11 20:18:23,634 INFO [galaxy.queue_worker] Sending reconfigure_watcher control task. -2021-03-11 20:18:23,679 INFO [galaxy.jobs.handler] sending stop signal to worker thread -2021-03-11 20:18:23,680 INFO [galaxy.jobs.handler] job handler queue stopped -2021-03-11 20:18:23,680 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 job worker threads -2021-03-11 20:18:23,680 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown... -2021-03-11 20:18:23,681 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly -2021-03-11 20:18:23,681 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 job worker threads -2021-03-11 20:18:23,681 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown... -2021-03-11 20:18:23,681 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly -2021-03-11 20:18:23,681 INFO [galaxy.jobs.handler] sending stop signal to worker thread -2021-03-11 20:18:23,682 INFO [galaxy.jobs.handler] job handler stop queue stopped -2021-03-11 20:18:23,682 INFO [test_driver] Application galaxy stopped. -Testing complete. HTML report is in "/home/rstudio/src/w4mclassfilter_galaxy_wrapper/tools/w4mclassfilter/tool_test_output.html". -All 13 test(s) executed passed. -w4mclassfilter (Test #1): passed -w4mclassfilter (Test #2): passed -w4mclassfilter (Test #3): passed -w4mclassfilter (Test #4): passed -w4mclassfilter (Test #5): passed -w4mclassfilter (Test #6): passed -w4mclassfilter (Test #7): passed -w4mclassfilter (Test #8): passed -w4mclassfilter (Test #9): passed -w4mclassfilter (Test #10): passed -w4mclassfilter (Test #11): passed -w4mclassfilter (Test #12): passed -w4mclassfilter (Test #13): passed diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/w4mclassfilter.xml --- a/tools/w4mclassfilter/w4mclassfilter.xml Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1114 +0,0 @@ - - Filter W4M data by values or metadata - - r-base - r-batch - w4mclassfilter - - &2); - [ ! 1 ]; - else - Rscript - $__tool_directory__/w4mclassfilter_wrapper.R - dataMatrix_in '$dataMatrix_in' - sampleMetadata_in '$sampleMetadata_in' - variableMetadata_in '$variableMetadata_in' - sampleclassNames '$sampleclassNames' - inclusive '$inclusive' - wildcards '$wildcards' - classnameColumn '$classnameColumn' - samplenameColumn 'sampleMetadata' - variable_range_filter '$variableRangeFilter' - transformation '$transformation' - imputation '$imputation' - dataMatrix_out '$dataMatrix_out' - sampleMetadata_out '$sampleMetadata_out' - variableMetadata_out '$variableMetadata_out' - order_vrbl '$order_vrbl' - order_smpl '$order_smpl' - centering '$centering'; - fi - ]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - é - - - 10.1093/bioinformatics/btu813 - - 10.1016/j.biocel.2017.07.002 - - 10.1021/ac202450g - - 10.1021/ac051437y - - 10.1021/acs.jproteome.5b00354 - - diff -r 1d36ecf93e67 -r 08d4ca8bc6dd tools/w4mclassfilter/w4mclassfilter_wrapper.R --- a/tools/w4mclassfilter/w4mclassfilter_wrapper.R Thu Mar 11 20:44:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,233 +0,0 @@ -#!/usr/bin/env Rscript - -library(batch) ## parseCommandArgs - -######## -# MAIN # -######## - -argVc <- unlist(parseCommandArgs(evaluate=FALSE)) - -##------------------------------ -## Initializing -##------------------------------ - -## options -##-------- - -strAsFacL <- options()$stringsAsFactors -options(stringsAsFactors = FALSE) - -## libraries -##---------- - -suppressMessages(library(w4mclassfilter)) - -expected_version <- "0.98.18" -actual_version <- packageVersion("w4mclassfilter") -if(packageVersion("w4mclassfilter") < expected_version) { - stop( - sprintf( - "Unrecoverable error: Version %s of the 'w4mclassfilter' R package was loaded instead of expected version %s", - actual_version, expected_version - ) - ) -} - -## constants -##---------- - -modNamC <- "w4mclassfilter" ## module name - -topEnvC <- environment() -flgC <- "\n" - -## functions -##---------- - -flgF <- function(tesC, - envC = topEnvC, - txtC = NA) { ## management of warning and error messages - - tesL <- eval(parse(text = tesC), envir = envC) - - if(!tesL) { - - #sink(NULL) - stpTxtC <- ifelse(is.na(txtC), - paste0(tesC, " is FALSE"), - txtC) - - stop(stpTxtC, - call. = FALSE) - - } - -} ## flgF - - -## log file -##--------- - -my_print <- function(x, ...) { cat(c(x, ...))} - -my_print("\nStart of the '", modNamC, "' Galaxy module call: ", - format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") - -## arguments -##---------- - -# files - -dataMatrix_in <- as.character(argVc["dataMatrix_in"]) -dataMatrix_out <- as.character(argVc["dataMatrix_out"]) - -sampleMetadata_in <- as.character(argVc["sampleMetadata_in"]) -sampleMetadata_out <- as.character(argVc["sampleMetadata_out"]) - -variableMetadata_in <- as.character(argVc["variableMetadata_in"]) -variableMetadata_out <- as.character(argVc["variableMetadata_out"]) - -# other parameters - -transformation <- as.character(argVc["transformation"]) -my_imputation_label <- as.character(argVc["imputation"]) -my_imputation_function <- if (my_imputation_label == "zero") { - w4m_filter_zero_imputation -} else if (my_imputation_label == "center") { - w4m_filter_median_imputation -} else if (my_imputation_label == "none") { - w4m_filter_no_imputation -} else { - stop(sprintf("Unknown value %s supplied for 'imputation' parameter. Expected one of {zero,center,none}.")) -} -wildcards <- as.logical(argVc["wildcards"]) -sampleclassNames <- as.character(argVc["sampleclassNames"]) -sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] -if (wildcards) { - sampleclassNames <- gsub("[.]", "[.]", sampleclassNames) - sampleclassNames <- utils::glob2rx(sampleclassNames, trim.tail = FALSE) -} -inclusive <- as.logical(argVc["inclusive"]) -classnameColumn <- as.character(argVc["classnameColumn"]) -samplenameColumn <- as.character(argVc["samplenameColumn"]) - -order_vrbl <- as.character(argVc["order_vrbl"]) -centering <- as.character(argVc["centering"]) -order_smpl <- - if (centering == 'centroid' || centering == 'median') { - "sampleMetadata" - } else { - as.character(argVc["order_smpl"]) - } - -variable_range_filter <- as.character(argVc["variable_range_filter"]) -variable_range_filter <- strsplit(x = variable_range_filter, split = ",", fixed = TRUE)[[1]] - -## ----------------------------- -## Transformation and imputation -## ----------------------------- -my_transformation_and_imputation <- if (transformation == "log10") { - function(m) { - # convert negative intensities to missing values - m[m < 0] <- NA - if (!is.matrix(m)) - stop("Cannot transform and impute data - the supplied data is not in matrix form") - if (nrow(m) == 0) - stop("Cannot transform and impute data - data matrix has no rows") - if (ncol(m) == 0) - stop("Cannot transform and impute data - data matrix has no columns") - suppressWarnings({ - # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step - m <- log10(m) - m[is.na(m)] <- NA - }) - return ( my_imputation_function(m) ) - } -} else if (transformation == "log2") { - function(m) { - # convert negative intensities to missing values - m[m < 0] <- NA - if (!is.matrix(m)) - stop("Cannot transform and impute data - the supplied data is not in matrix form") - if (nrow(m) == 0) - stop("Cannot transform and impute data - data matrix has no rows") - if (ncol(m) == 0) - stop("Cannot transform and impute data - data matrix has no columns") - suppressWarnings({ - # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step - m <- log2(m) - m[is.na(m)] <- NA - }) - return ( my_imputation_function(m) ) - } -} else { - function(m) { - # convert negative intensities to missing values - m[m < 0] <- NA - if (!is.matrix(m)) - stop("Cannot transform and impute data - the supplied data is not in matrix form") - if (nrow(m) == 0) - stop("Cannot transform and impute data - data matrix has no rows") - if (ncol(m) == 0) - stop("Cannot transform and impute data - data matrix has no columns") - suppressWarnings({ - # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step - m[is.na(m)] <- NA - }) - return ( my_imputation_function(m) ) - } -} - -##------------------------------ -## Computation -##------------------------------ - -result <- w4m_filter_by_sample_class( - dataMatrix_in = dataMatrix_in -, sampleMetadata_in = sampleMetadata_in -, variableMetadata_in = variableMetadata_in -, dataMatrix_out = dataMatrix_out -, sampleMetadata_out = sampleMetadata_out -, variableMetadata_out = variableMetadata_out -, classes = sampleclassNames -, include = inclusive -, class_column = classnameColumn -, samplename_column = samplenameColumn -, order_vrbl = order_vrbl -, order_smpl = order_smpl -, centering = centering -, variable_range_filter = variable_range_filter -, failure_action = my_print -, data_imputation = my_transformation_and_imputation -) - -my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ", - as.character(result), "\n", sep = "") - -##-------- -## Closing -##-------- - -my_print("\nEnd of '", modNamC, "' Galaxy module call: ", - as.character(Sys.time()), "\n", sep = "") - -#sink() - -if (!file.exists(dataMatrix_out)) { - print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, dataMatrix_out)) -}# else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, dataMatrix_out)) } - -if (!file.exists(variableMetadata_out)) { - print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, variableMetadata_out)) -} # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, variableMetadata_out)) } - -if (!file.exists(sampleMetadata_out)) { - print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, sampleMetadata_out)) -} # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, sampleMetadata_out)) } - -if( !result ) { - stop(sprintf("ERROR %s::w4m_filter_by_sample_class - method failed", modNamC)) -} - -rm(list = ls()) diff -r 1d36ecf93e67 -r 08d4ca8bc6dd w4mclassfilter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/w4mclassfilter.xml Thu Mar 11 20:46:26 2021 +0000 @@ -0,0 +1,1114 @@ + + Filter W4M data by values or metadata + + r-base + r-batch + w4mclassfilter + + &2); + [ ! 1 ]; + else + Rscript + $__tool_directory__/w4mclassfilter_wrapper.R + dataMatrix_in '$dataMatrix_in' + sampleMetadata_in '$sampleMetadata_in' + variableMetadata_in '$variableMetadata_in' + sampleclassNames '$sampleclassNames' + inclusive '$inclusive' + wildcards '$wildcards' + classnameColumn '$classnameColumn' + samplenameColumn 'sampleMetadata' + variable_range_filter '$variableRangeFilter' + transformation '$transformation' + imputation '$imputation' + dataMatrix_out '$dataMatrix_out' + sampleMetadata_out '$sampleMetadata_out' + variableMetadata_out '$variableMetadata_out' + order_vrbl '$order_vrbl' + order_smpl '$order_smpl' + centering '$centering'; + fi + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + é + + + 10.1093/bioinformatics/btu813 + + 10.1016/j.biocel.2017.07.002 + + 10.1021/ac202450g + + 10.1021/ac051437y + + 10.1021/acs.jproteome.5b00354 + + diff -r 1d36ecf93e67 -r 08d4ca8bc6dd w4mclassfilter_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/w4mclassfilter_wrapper.R Thu Mar 11 20:46:26 2021 +0000 @@ -0,0 +1,233 @@ +#!/usr/bin/env Rscript + +library(batch) ## parseCommandArgs + +######## +# MAIN # +######## + +argVc <- unlist(parseCommandArgs(evaluate=FALSE)) + +##------------------------------ +## Initializing +##------------------------------ + +## options +##-------- + +strAsFacL <- options()$stringsAsFactors +options(stringsAsFactors = FALSE) + +## libraries +##---------- + +suppressMessages(library(w4mclassfilter)) + +expected_version <- "0.98.18" +actual_version <- packageVersion("w4mclassfilter") +if(packageVersion("w4mclassfilter") < expected_version) { + stop( + sprintf( + "Unrecoverable error: Version %s of the 'w4mclassfilter' R package was loaded instead of expected version %s", + actual_version, expected_version + ) + ) +} + +## constants +##---------- + +modNamC <- "w4mclassfilter" ## module name + +topEnvC <- environment() +flgC <- "\n" + +## functions +##---------- + +flgF <- function(tesC, + envC = topEnvC, + txtC = NA) { ## management of warning and error messages + + tesL <- eval(parse(text = tesC), envir = envC) + + if(!tesL) { + + #sink(NULL) + stpTxtC <- ifelse(is.na(txtC), + paste0(tesC, " is FALSE"), + txtC) + + stop(stpTxtC, + call. = FALSE) + + } + +} ## flgF + + +## log file +##--------- + +my_print <- function(x, ...) { cat(c(x, ...))} + +my_print("\nStart of the '", modNamC, "' Galaxy module call: ", + format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") + +## arguments +##---------- + +# files + +dataMatrix_in <- as.character(argVc["dataMatrix_in"]) +dataMatrix_out <- as.character(argVc["dataMatrix_out"]) + +sampleMetadata_in <- as.character(argVc["sampleMetadata_in"]) +sampleMetadata_out <- as.character(argVc["sampleMetadata_out"]) + +variableMetadata_in <- as.character(argVc["variableMetadata_in"]) +variableMetadata_out <- as.character(argVc["variableMetadata_out"]) + +# other parameters + +transformation <- as.character(argVc["transformation"]) +my_imputation_label <- as.character(argVc["imputation"]) +my_imputation_function <- if (my_imputation_label == "zero") { + w4m_filter_zero_imputation +} else if (my_imputation_label == "center") { + w4m_filter_median_imputation +} else if (my_imputation_label == "none") { + w4m_filter_no_imputation +} else { + stop(sprintf("Unknown value %s supplied for 'imputation' parameter. Expected one of {zero,center,none}.")) +} +wildcards <- as.logical(argVc["wildcards"]) +sampleclassNames <- as.character(argVc["sampleclassNames"]) +sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] +if (wildcards) { + sampleclassNames <- gsub("[.]", "[.]", sampleclassNames) + sampleclassNames <- utils::glob2rx(sampleclassNames, trim.tail = FALSE) +} +inclusive <- as.logical(argVc["inclusive"]) +classnameColumn <- as.character(argVc["classnameColumn"]) +samplenameColumn <- as.character(argVc["samplenameColumn"]) + +order_vrbl <- as.character(argVc["order_vrbl"]) +centering <- as.character(argVc["centering"]) +order_smpl <- + if (centering == 'centroid' || centering == 'median') { + "sampleMetadata" + } else { + as.character(argVc["order_smpl"]) + } + +variable_range_filter <- as.character(argVc["variable_range_filter"]) +variable_range_filter <- strsplit(x = variable_range_filter, split = ",", fixed = TRUE)[[1]] + +## ----------------------------- +## Transformation and imputation +## ----------------------------- +my_transformation_and_imputation <- if (transformation == "log10") { + function(m) { + # convert negative intensities to missing values + m[m < 0] <- NA + if (!is.matrix(m)) + stop("Cannot transform and impute data - the supplied data is not in matrix form") + if (nrow(m) == 0) + stop("Cannot transform and impute data - data matrix has no rows") + if (ncol(m) == 0) + stop("Cannot transform and impute data - data matrix has no columns") + suppressWarnings({ + # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step + m <- log10(m) + m[is.na(m)] <- NA + }) + return ( my_imputation_function(m) ) + } +} else if (transformation == "log2") { + function(m) { + # convert negative intensities to missing values + m[m < 0] <- NA + if (!is.matrix(m)) + stop("Cannot transform and impute data - the supplied data is not in matrix form") + if (nrow(m) == 0) + stop("Cannot transform and impute data - data matrix has no rows") + if (ncol(m) == 0) + stop("Cannot transform and impute data - data matrix has no columns") + suppressWarnings({ + # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step + m <- log2(m) + m[is.na(m)] <- NA + }) + return ( my_imputation_function(m) ) + } +} else { + function(m) { + # convert negative intensities to missing values + m[m < 0] <- NA + if (!is.matrix(m)) + stop("Cannot transform and impute data - the supplied data is not in matrix form") + if (nrow(m) == 0) + stop("Cannot transform and impute data - data matrix has no rows") + if (ncol(m) == 0) + stop("Cannot transform and impute data - data matrix has no columns") + suppressWarnings({ + # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step + m[is.na(m)] <- NA + }) + return ( my_imputation_function(m) ) + } +} + +##------------------------------ +## Computation +##------------------------------ + +result <- w4m_filter_by_sample_class( + dataMatrix_in = dataMatrix_in +, sampleMetadata_in = sampleMetadata_in +, variableMetadata_in = variableMetadata_in +, dataMatrix_out = dataMatrix_out +, sampleMetadata_out = sampleMetadata_out +, variableMetadata_out = variableMetadata_out +, classes = sampleclassNames +, include = inclusive +, class_column = classnameColumn +, samplename_column = samplenameColumn +, order_vrbl = order_vrbl +, order_smpl = order_smpl +, centering = centering +, variable_range_filter = variable_range_filter +, failure_action = my_print +, data_imputation = my_transformation_and_imputation +) + +my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ", + as.character(result), "\n", sep = "") + +##-------- +## Closing +##-------- + +my_print("\nEnd of '", modNamC, "' Galaxy module call: ", + as.character(Sys.time()), "\n", sep = "") + +#sink() + +if (!file.exists(dataMatrix_out)) { + print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, dataMatrix_out)) +}# else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, dataMatrix_out)) } + +if (!file.exists(variableMetadata_out)) { + print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, variableMetadata_out)) +} # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, variableMetadata_out)) } + +if (!file.exists(sampleMetadata_out)) { + print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, sampleMetadata_out)) +} # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, sampleMetadata_out)) } + +if( !result ) { + stop(sprintf("ERROR %s::w4m_filter_by_sample_class - method failed", modNamC)) +} + +rm(list = ls())