Mercurial > repos > p.lucas > clermontyping

changeset 2:07fe3c343426 draft

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wrapper with all packages
author p.lucas
date Mon, 14 Feb 2022 14:40:43 +0000
parents cec55ef9cce5
children 01234c8a9353
files ClermonTyping_wrapper.xml
diffstat 1 files changed, 175 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/ClermonTyping_wrapper.xml	Mon Feb 14 14:20:05 2022 +0000
+++ b/ClermonTyping_wrapper.xml	Mon Feb 14 14:40:43 2022 +0000
@@ -2,10 +2,182 @@
   <description>
     ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping
   </description>
+  <requirements>
+    <requirement type="package" version="0.1">_libgcc_mutex</requirement>
+    <requirement type="package" version="4.5">_openmp_mutex</requirement>
+    <requirement type="package" version="1.0.1">_r-mutex</requirement>
+    <requirement type="package" version="2.35.1">binutils_impl_linux-64</requirement>
+    <requirement type="package" version="2.35.1">binutils_linux-64</requirement>
+    <requirement type="package" version="1.79">biopython</requirement>
+    <requirement type="package" version="2.12.0">blast</requirement>
+    <requirement type="package" version="1.9.14">bwidget</requirement>
+    <requirement type="package" version="1.0.8">bzip2</requirement>
+    <requirement type="package" version="1.18.1">c-ares</requirement>
+    <requirement type="package" version="2021.10.8">ca-certificates</requirement>
+    <requirement type="package" version="1.16.0">cairo</requirement>
+    <requirement type="package" version="7.81.0">curl</requirement>
+    <requirement type="package" version="16.2">entrez-direct</requirement>
+    <requirement type="package" version="2.37">font-ttf-dejavu-sans-mono</requirement>
+    <requirement type="package" version="3.000">font-ttf-inconsolata</requirement>
+    <requirement type="package" version="2.038">font-ttf-source-code-pro</requirement>
+    <requirement type="package" version="0.83">font-ttf-ubuntu</requirement>
+    <requirement type="package" version="2.13.96">fontconfig</requirement>
+    <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
+    <requirement type="package" version="1">fonts-conda-forge</requirement>
+    <requirement type="package" version="2.10.4">freetype</requirement>
+    <requirement type="package" version="1.0.10">fribidi</requirement>
+    <requirement type="package" version="9.3.0">gcc_impl_linux-64</requirement>
+    <requirement type="package" version="9.3.0">gcc_linux-64</requirement>
+    <requirement type="package" version="0.19.8.1">gettext</requirement>
+    <requirement type="package" version="9.3.0">gfortran_impl_linux-64</requirement>
+    <requirement type="package" version="9.3.0">gfortran_linux-64</requirement>
+    <requirement type="package" version="1.3.13">graphite2</requirement>
+    <requirement type="package" version="2.6">gsl</requirement>
+    <requirement type="package" version="9.3.0">gxx_impl_linux-64</requirement>
+    <requirement type="package" version="9.3.0">gxx_linux-64</requirement>
+    <requirement type="package" version="2.9.1">harfbuzz</requirement>
+    <requirement type="package" version="68.2">icu</requirement>
+    <requirement type="package" version="2.1">jbig</requirement>
+    <requirement type="package" version="9e">jpeg</requirement>
+    <requirement type="package" version="2.6.32">kernel-headers_linux-64</requirement>
+    <requirement type="package" version="1.19.2">krb5</requirement>
+    <requirement type="package" version="2.35.1">ld_impl_linux-64</requirement>
+    <requirement type="package" version="3.0">lerc</requirement>
+    <requirement type="package" version="3.9.0">libblas</requirement>
+    <requirement type="package" version="3.9.0">libcblas</requirement>
+    <requirement type="package" version="7.81.0">libcurl</requirement>
+    <requirement type="package" version="1.8">libdeflate</requirement>
+    <requirement type="package" version="3.1.20191231">libedit</requirement>
+    <requirement type="package" version="4.33">libev</requirement>
+    <requirement type="package" version="3.4.2">libffi</requirement>
+    <requirement type="package" version="9.3.0">libgcc-devel_linux-64</requirement>
+    <requirement type="package" version="11.2.0">libgcc-ng</requirement>
+    <requirement type="package" version="9.3.0">libgfortran-ng</requirement>
+    <requirement type="package" version="9.3.0">libgfortran5</requirement>
+    <requirement type="package" version="2.70.2">libglib</requirement>
+    <requirement type="package" version="11.2.0">libgomp</requirement>
+    <requirement type="package" version="1.16">libiconv</requirement>
+    <requirement type="package" version="3.9.0">liblapack</requirement>
+    <requirement type="package" version="1.46.0">libnghttp2</requirement>
+    <requirement type="package" version="2.0.0">libnsl</requirement>
+    <requirement type="package" version="0.3.17">libopenblas</requirement>
+    <requirement type="package" version="1.6.37">libpng</requirement>
+    <requirement type="package" version="1.10.0">libssh2</requirement>
+    <requirement type="package" version="9.3.0">libstdcxx-devel_linux-64</requirement>
+    <requirement type="package" version="11.2.0">libstdcxx-ng</requirement>
+    <requirement type="package" version="4.3.0">libtiff</requirement>
+    <requirement type="package" version="2.32.1">libuuid</requirement>
+    <requirement type="package" version="1.2.2">libwebp-base</requirement>
+    <requirement type="package" version="1.13">libxcb</requirement>
+    <requirement type="package" version="2.9.12">libxml2</requirement>
+    <requirement type="package" version="1.2.11">libzlib</requirement>
+    <requirement type="package" version="1.9.3">lz4-c</requirement>
+    <requirement type="package" version="4.3">make</requirement>
+    <requirement type="package" version="6.3">ncurses</requirement>
+    <requirement type="package" version="1.22.2">numpy</requirement>
+    <requirement type="package" version="3.0.0">openssl</requirement>
+    <requirement type="package" version="2.17.1.1">pandoc</requirement>
+    <requirement type="package" version="1.48.10">pango</requirement>
+    <requirement type="package" version="8.45">pcre</requirement>
+    <requirement type="package" version="10.37">pcre2</requirement>
+    <requirement type="package" version="5.32.1">perl</requirement>
+    <requirement type="package" version="2.40">perl-archive-tar</requirement>
+    <requirement type="package" version="1.50">perl-carp</requirement>
+    <requirement type="package" version="3.75">perl-common-sense</requirement>
+    <requirement type="package" version="2.101">perl-compress-raw-bzip2</requirement>
+    <requirement type="package" version="2.101">perl-compress-raw-zlib</requirement>
+    <requirement type="package" version="5.74">perl-exporter</requirement>
+    <requirement type="package" version="1.002002">perl-exporter-tiny</requirement>
+    <requirement type="package" version="7.64">perl-extutils-makemaker</requirement>
+    <requirement type="package" version="2.087">perl-io-compress</requirement>
+    <requirement type="package" version="1.10">perl-io-zlib</requirement>
+    <requirement type="package" version="4.05">perl-json</requirement>
+    <requirement type="package" version="2.34">perl-json-xs</requirement>
+    <requirement type="package" version="0.428">perl-list-moreutils</requirement>
+    <requirement type="package" version="0.430">perl-list-moreutils-xs</requirement>
+    <requirement type="package" version="3.75">perl-pathtools</requirement>
+    <requirement type="package" version="1.60">perl-scalar-list-utils</requirement>
+    <requirement type="package" version="1.01">perl-types-serialiser</requirement>
+    <requirement type="package" version="22.0.3">pip</requirement>
+    <requirement type="package" version="0.40.0">pixman</requirement>
+    <requirement type="package" version="0.4">pthread-stubs</requirement>
+    <requirement type="package" version="3.8.12">python</requirement>
+    <requirement type="package" version="3.8">python_abi</requirement>
+    <requirement type="package" version="0.2.1">r-assertthat</requirement>
+    <requirement type="package" version="4.0.5">r-base</requirement>
+    <requirement type="package" version="0.1_3">r-base64enc</requirement>
+    <requirement type="package" version="4.0.4">r-bit</requirement>
+    <requirement type="package" version="4.0.5">r-bit64</requirement>
+    <requirement type="package" version="3.1.1">r-cli</requirement>
+    <requirement type="package" version="0.7.1">r-clipr</requirement>
+    <requirement type="package" version="0.4.2">r-cpp11</requirement>
+    <requirement type="package" version="1.4.2">r-crayon</requirement>
+    <requirement type="package" version="0.6.29">r-digest</requirement>
+    <requirement type="package" version="1.0.7">r-dplyr</requirement>
+    <requirement type="package" version="0.3.2">r-ellipsis</requirement>
+    <requirement type="package" version="0.14">r-evaluate</requirement>
+    <requirement type="package" version="1.0.2">r-fansi</requirement>
+    <requirement type="package" version="1.1.0">r-fastmap</requirement>
+    <requirement type="package" version="0.1.2">r-generics</requirement>
+    <requirement type="package" version="1.6.1">r-glue</requirement>
+    <requirement type="package" version="0.9">r-highr</requirement>
+    <requirement type="package" version="1.1.1">r-hms</requirement>
+    <requirement type="package" version="0.5.2">r-htmltools</requirement>
+    <requirement type="package" version="0.1.4">r-jquerylib</requirement>
+    <requirement type="package" version="1.7.3">r-jsonlite</requirement>
+    <requirement type="package" version="1.37">r-knitr</requirement>
+    <requirement type="package" version="1.0.1">r-lifecycle</requirement>
+    <requirement type="package" version="2.0.2">r-magrittr</requirement>
+    <requirement type="package" version="1.1">r-markdown</requirement>
+    <requirement type="package" version="0.12">r-mime</requirement>
+    <requirement type="package" version="1.7.0">r-pillar</requirement>
+    <requirement type="package" version="2.0.3">r-pkgconfig</requirement>
+    <requirement type="package" version="1.1.1">r-prettyunits</requirement>
+    <requirement type="package" version="1.2.2">r-progress</requirement>
+    <requirement type="package" version="0.3.4">r-purrr</requirement>
+    <requirement type="package" version="2.5.1">r-r6</requirement>
+    <requirement type="package" version="2.1.2">r-readr</requirement>
+    <requirement type="package" version="0.4.12">r-rlang</requirement>
+    <requirement type="package" version="2.11">r-rmarkdown</requirement>
+    <requirement type="package" version="1.7.6">r-stringi</requirement>
+    <requirement type="package" version="1.4.0">r-stringr</requirement>
+    <requirement type="package" version="3.1.6">r-tibble</requirement>
+    <requirement type="package" version="1.2.0">r-tidyr</requirement>
+    <requirement type="package" version="1.1.1">r-tidyselect</requirement>
+    <requirement type="package" version="0.36">r-tinytex</requirement>
+    <requirement type="package" version="0.2.0">r-tzdb</requirement>
+    <requirement type="package" version="1.2.2">r-utf8</requirement>
+    <requirement type="package" version="0.3.8">r-vctrs</requirement>
+    <requirement type="package" version="1.5.7">r-vroom</requirement>
+    <requirement type="package" version="2.4.3">r-withr</requirement>
+    <requirement type="package" version="0.29">r-xfun</requirement>
+    <requirement type="package" version="2.2.2">r-yaml</requirement>
+    <requirement type="package" version="8.1">readline</requirement>
+    <requirement type="package" version="4.8">sed</requirement>
+    <requirement type="package" version="60.8.1">setuptools</requirement>
+    <requirement type="package" version="3.37.0">sqlite</requirement>
+    <requirement type="package" version="2.12">sysroot_linux-64</requirement>
+    <requirement type="package" version="8.6.11">tk</requirement>
+    <requirement type="package" version="2.10">tktable</requirement>
+    <requirement type="package" version="0.37.1">wheel</requirement>
+    <requirement type="package" version="1.0.7">xorg-kbproto</requirement>
+    <requirement type="package" version="1.0.10">xorg-libice</requirement>
+    <requirement type="package" version="1.2.3">xorg-libsm</requirement>
+    <requirement type="package" version="1.7.2">xorg-libx11</requirement>
+    <requirement type="package" version="1.0.9">xorg-libxau</requirement>
+    <requirement type="package" version="1.1.3">xorg-libxdmcp</requirement>
+    <requirement type="package" version="1.3.4">xorg-libxext</requirement>
+    <requirement type="package" version="0.9.10">xorg-libxrender</requirement>
+    <requirement type="package" version="1.2.1">xorg-libxt</requirement>
+    <requirement type="package" version="0.11.1">xorg-renderproto</requirement>
+    <requirement type="package" version="7.3.0">xorg-xextproto</requirement>
+    <requirement type="package" version="7.0.31">xorg-xproto</requirement>
+    <requirement type="package" version="5.2.5">xz</requirement>
+    <requirement type="package" version="1.2.11">zlib</requirement>
+    <requirement type="package" version="1.5.2">zstd</requirement>
+  </requirements>
   <command detect_errors="exit_code"><![CDATA[
-    source /home/galaxy/data/_conda/bin/activate Ab-HADDOCK;
-    /home/galaxy/ClermonTyping/clermonTyping.sh --fasta ${input} --name Analyse;
-    source /home/galaxy/data/_conda/bin/deactivate;
+    /home/galaxy/ClermonTyping/clermonTyping.sh --fasta ${input} --name Analyse
   ]]></command>
   <inputs>
     <param name="input" format="fasta" type="data" label="Select contigs file in fasta format." help="Fasta format containing contigs."/>