Mercurial > repos > brasset_jensen > srnapipe

changeset 52:b62dc0435760 draft

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Uploaded
author pierre.pouchin
date Thu, 06 Sep 2018 11:59:18 -0400
parents 1d7d33c46375
children c9fa369b0b79
files sRNAPipe.xml tool_dependencies.xml
diffstat 2 files changed, 11 insertions(+), 48 deletions(-) [+]
line wrap: on
line diff
--- a/sRNAPipe.xml	Thu Sep 06 11:43:21 2018 -0400
+++ b/sRNAPipe.xml	Thu Sep 06 11:59:18 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="sRNAPipe" name="sRNAPipe" version="1.0">
+<tool id="sRNAPipe" name="sRNAPipe" version="0.0.1">
   <description>In-depth study of small RNA</description>
   <command interpreter="perl">
 
@@ -84,8 +84,16 @@
     <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</requirement>
-    <requirement type="package" version="5.18.1">perl</requirement>
+    <requirement type="package" version="3.3.2">r-base</requirement>
+    <requirement type="package" version="5.20.3.1">perl</requirement>
+    <requirement type="package" version="2.50">perl-getopt-long</requirement>
+    <requirement type="package" version="1.19">perl-parallel-forkmanager</requirement>
+    <requirement type="package" version="0.34" >perl-statistics-r</requirement>
+    <requirement type="package" version="0.29">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-colorbrewer</requirement>
+    <requirement type="package" version="1.0.1">r-ggplot2</requirement>
   </requirements> 
 
   <inputs>
--- a/tool_dependencies.xml	Thu Sep 06 11:43:21 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-<?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>