# HG changeset patch # User peterjc # Date 1431446199 14400 # Node ID dbd5a2b27735ee5051b92a602cf39461f7438e7f # Parent a8c978f17251b893a168d51bfc0f9aab2c2c6ce8 planemo upload for https://github.com/peterjc/pico_galaxy/tools/clinod/a231f86098ffe01436298bb07ba857ec8bf6cee0 diff -r a8c978f17251 -r dbd5a2b27735 tools/clinod/README.rst --- a/tools/clinod/README.rst Thu Nov 20 06:14:45 2014 -0500 +++ b/tools/clinod/README.rst Tue May 12 11:56:39 2015 -0400 @@ -1,7 +1,7 @@ Galaxy wrapper for Command line NoD predictor (v1.3) ==================================================== -This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute +This wrapper is copyright 2011-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. @@ -70,6 +70,8 @@ - Development moved to GitHub, https://github.com/peterjc/pico_galaxy v0.0.7 - Use the new ``$GALAXY_SLOTS`` environment variable for thread count. - Tool definition now embeds citation information. +v0.0.8 - Reorder XML elements (internal change only). + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). ======= ====================================================================== @@ -82,19 +84,28 @@ Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder:: +For pushing a release to the test or main "Galaxy Tool Shed", use the following +Planemo commands (which requires you have set your Tool Shed access details in +``~/.planemo.yml`` and that you have access rights on the Tool Shed):: + + $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clinod/ + ... + +or:: - $ tar -czf clinod.tar.gz tools/clinod/README.rst tools/clinod/clinod.xml tools/clinod/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular + $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/clinod/ + ... + +To just build and check the tar ball, use:: -Check this worked:: - - $ tar -tzf clinod.tar.gz + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/clinod/ + ... + $ tar -tzf shed_upload.tar.gz + test-data/four_human_proteins.fasta + test-data/four_human_proteins.clinod-1.3.tabular tools/clinod/README.rst tools/clinod/clinod.xml tools/clinod/tool_dependencies.xml - test-data/four_human_proteins.fasta - test-data/four_human_proteins.clinod-1.3.tabular Licence (MIT) diff -r a8c978f17251 -r dbd5a2b27735 tools/clinod/clinod.xml --- a/tools/clinod/clinod.xml Thu Nov 20 06:14:45 2014 -0500 +++ b/tools/clinod/clinod.xml Tue May 12 11:56:39 2015 -0400 @@ -1,20 +1,20 @@ - + Find nucleolar localization signals (NoLSs) in protein sequences java clinod + + + + + ##The Galaxy Tool Shed installation should define $CLINOD to point at folder ##containing both clinod-1.3.jar and the batchman binary: java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence ##TODO - Make the -clean_sequence argument a parameter? - - - - - diff -r a8c978f17251 -r dbd5a2b27735 tools/clinod/tool_dependencies.xml --- a/tools/clinod/tool_dependencies.xml Thu Nov 20 06:14:45 2014 -0500 +++ b/tools/clinod/tool_dependencies.xml Tue May 12 11:56:39 2015 -0400 @@ -22,7 +22,7 @@ Downloads and installs the command line NoD (clinod) JAR file and the binary dependency batchman, and sets $CLINOD to the folder used. -We could download, compiles and install the SNNS Batch Interpreter v1.0 executable +We could download, compile and install the SNNS Batch Interpreter v1.0 executable (batchman) from Stuttgart Neural Network Simulator (SNNS) v4.2. However, we simplify this by downloading SNNS v4.3 which includes the precompiled copy of batch man.