Mercurial > repos > fubar > edger_test

changeset 29:81255a103a8c draft

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Uploaded
author fubar
date Wed, 12 Jun 2013 23:23:05 -0400
parents a0c04d13a7cf
children 061259d5e6e4
files rgedgeR/test-data/gentestdata.sh~ rgedgeR/tool_dependencies.xml rgedgeR/tool_dependencies.xml~
diffstat 3 files changed, 3 insertions(+), 33 deletions(-) [+]
line wrap: on
line diff
--- a/rgedgeR/test-data/gentestdata.sh~	Wed Jun 12 21:47:08 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-#!/bin/bash
-# generate test data for rgGSEA
-# ross lazarus June 2013 
-# adjust gseajar_path !
-GSEAJAR_PATH=/home/rlazarus/galaxy-central/tool_dependency_dir/gsea_jar/2.0.12/fubar/rg_gsea_test/8e291f464aa0/jars/gsea2-2.0.12.jar
-python ../rgGSEA.py --input_tab "gsea_test_DGE.xls"  --adjpvalcol "5" --signcol "2" --idcol "1" --outhtml "gseatestout.html" --input_name "gsea_test" --setMax "500" --setMin "15" --nPerm "10" --plotTop "20" --gsea_jar "$GSEAJAR_PATH" --output_dir "gseatestout" --mode "Max_probe" --title "GSEA test" --builtin_gmt "gseatestdata.gmt"
-
-
--- a/rgedgeR/tool_dependencies.xml	Wed Jun 12 21:47:08 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Wed Jun 12 23:23:05 2013 -0400
@@ -1,17 +1,17 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="r3" version="3.0.1">
-        <repository changeset_revision="b90bcba24d6a" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="addf8c9c778a" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="biocbasics" version="2.12">
         <install version="1.0"> 
             <actions>
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="b90bcba24d6a" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                    <repository changeset_revision="addf8c9c778a" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                         <package name="r3" version="3.0.1" />
                     </repository>
                 </action>
-                <action type="shell_command">$R_HOME/R CMD BATCH installBioC.R </action>
+                <action type="shell_command">R CMD BATCH installBioC.R </action>
             </actions>
         </install>
         <readme>Installs some basic bioc packages for the edgeR tool
--- a/rgedgeR/tool_dependencies.xml~	Wed Jun 12 21:47:08 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="r3" version="3.0.1">
-        <repository changeset_revision="8dcdf371a760" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-    </package>
-    <package name="biocbasics" version="2.12">
-        <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">
-                            <repository name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-                        </package>
-                    
-                </action>
-                <action type="shell_command">$R_HOME/R CMD BATCH installBioC.R </action>
-            </actions>
-        </install>
-        <readme>Installs some basic bioc packages for the edgeR tool
-
-       </readme>
-    </package>
-</tool_dependency>