Mercurial > repos > brasset_jensen > srnapipe

changeset 51:1d7d33c46375 draft

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Uploaded
author pierre.pouchin
date Thu, 06 Sep 2018 11:43:21 -0400
parents 372ce358ef09
children b62dc0435760
files sRNAPipe.xml tool_dependencies.xml
diffstat 2 files changed, 46 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/sRNAPipe.xml	Thu Sep 06 11:25:35 2018 -0400
+++ b/sRNAPipe.xml	Thu Sep 06 11:43:21 2018 -0400
@@ -84,16 +84,8 @@
     <requirement type="package" version="0.7.12">bwa</requirement>
     <requirement type="package" version="2.24">bedtools</requirement>
     <requirement type="package" version="1.2">samtools</requirement>
-    <requirement type="package" version="3.2.1">r-base</requirement>
+    <requirement type="package" version="3.2.1">R</requirement>
     <requirement type="package" version="5.18.1">perl</requirement>
-    <requirement type="package" version="2.50">perl-getopt-long</requirement>
-    <requirement type="package" version="1.17">perl-parallel-forkmanager</requirement>
-    <requirement type="package" version="0.34" >perl-statistics-r</requirement>
-    <requirement type="package" version="0.30">perl-string-random</requirement>
-    <requirement type="package" version="3.6">r-plotrix</requirement>
-    <requirement type="package" version="1.14.0">bioconductor-sushi</requirement>
-    <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
-    <requirement type="package" version="2.2.1">r-ggplot2</requirement>
   </requirements> 
 
   <inputs>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Sep 06 11:43:21 2018 -0400
@@ -0,0 +1,45 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="bwa" version="0.7.12">
+    <repository changeset_revision="dcae4134cd62" name="package_bwa_0_7_12" owner="avowinkel" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="bedtools" version="2.24">
+    <repository changeset_revision="3416a1d4a582" name="package_bedtools_2_24" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="samtools" version="1.2">
+    <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="R" version="3.2.1">
+    <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <install version="1.0">
+      <actions>
+        <action type="setup_r_environment">
+          <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+            <package name="R" version="3.2.1" />
+          </repository>
+          <package>https://depot.galaxyproject.org/software/plotrix/plotrix_3.6_src_all.tar.gz</package>
+          <package>https://depot.galaxyproject.org/software/bioconductor-sushi/bioconductor-sushi_1.14.0_src_all.tar.gz</package>
+          <package>https://depot.galaxyproject.org/software/RColorBrewer/RColorBrewer_1.1-2_src_all.tar.gz</package>
+          <package>https://depot.galaxyproject.org/software/ggplot2/ggplot2_1.0.1_src_all.tar.gz</package>
+          <package>https://depot.galaxyproject.org/software/perl-statistics-r/perl-statistics-r_0.34_src_all.tar.gz</package>
+        </action>
+      </actions>
+    </install>
+  </package>
+  <package name="perl" version="5.18.1">
+    <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <install version="1.0">
+      <actions>
+        <action type="setup_perl_environment">
+          <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+            <package name="perl" version="5.18.1" />
+          </repository>
+          <package>https://cpan.metacpan.org/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz</package>
+          <package>https://cpan.metacpan.org/authors/id/F/FA/FANGLY/Statistics-R-0.34.tar.gz</package>
+          <package>https://cpan.metacpan.org/authors/id/J/JV/JV/Getopt-Long-2.50.tar.gz</package>
+          <package>https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/String-Random-0.29.tar.gz</package>
+        </action>
+      </actions>
+    </install>
+  </package>
+</tool_dependency>