Mercurial > repos > fubar > edger_test

changeset 19:0d6a14ee7c81 draft

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Uploaded
author fubar
date Wed, 12 Jun 2013 08:37:25 -0400 (2013-06-12)
parents 3f316c8adf4c
children 3b3066dea1a7
files rgedgeR/rgedgeRpaired.xml rgedgeR/tool_dependencies.xml
diffstat 2 files changed, 4 insertions(+), 7 deletions(-) [+]
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line diff
--- a/rgedgeR/rgedgeRpaired.xml	Wed Jun 12 08:17:26 2013 -0400
+++ b/rgedgeR/rgedgeRpaired.xml	Wed Jun 12 08:37:25 2013 -0400
@@ -1,9 +1,8 @@
 <tool id="rgedgeRpaired" name="edgeR" version="0.18">
   <description>1 or 2 level models for count data</description>
   <requirements>
-      <requirement type="package" version="3.0.1">package_R3</requirement>
+      <requirement type="package" version="3.0.1">R3</requirement>
       <requirement type="package" version="2.12">package_BioCBasics</requirement>
-      <requirement type="set_environment">R_SCRIPT_PATH</requirement>
   </requirements>
   
   <command interpreter="python">
--- a/rgedgeR/tool_dependencies.xml	Wed Jun 12 08:17:26 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Wed Jun 12 08:37:25 2013 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="package_BioCBasics" version="2.12">
-        <install version="1.0">
+        <install version="1.0"> 
             <actions>
                 <action type="set_environment_for_install">
                       <package name="R3" toolshed="http://testtoolshed.g2.bx.psu.edu" version="3.0.1">
@@ -12,10 +12,8 @@
                 <action type="shell_command">$R_HOME/R CMD BATCH installBioC.R </action>
             </actions>
         </install>
-        <readme>R is a free software environment for statistical computing and graphics
-                WARNING: See custom compilation options above
-                Modified from an older version of R by Boris by Ross Lazarus for R 3.0
-                Added Bioc basics via this package installBioC.R script
+        <readme>Installs some basic bioc packages for the edgeR tool
+
        </readme>
     </package>
 </tool_dependency>