# HG changeset patch
# User fubar
# Date 1371081483 14400
# Node ID db24a3130845d2cc3bc7ccd2eb8845e6b78871a7
# Parent  5526071146552deaed4c8e2b0cccb9f1bf8a0056
Uploaded

diff -r 552607114655 -r db24a3130845 rgedgeR/test-data/gentestdata.sh~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgedgeR/test-data/gentestdata.sh~	Wed Jun 12 19:58:03 2013 -0400
@@ -0,0 +1,8 @@
+#!/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 "$GSEAJAR_PATH" --output_dir "gseatestout" --mode "Max_probe" --title "GSEA test" --builtin_gmt "gseatestdata.gmt"
+
+
diff -r 552607114655 -r db24a3130845 rgedgeR/tool_dependencies.xml
--- a/rgedgeR/tool_dependencies.xml	Wed Jun 12 19:27:29 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Wed Jun 12 19:58:03 2013 -0400
@@ -1,16 +1,15 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="r3" version="3.0.1">
-        <repository changeset_revision="8dcdf371a760" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="8f91c9b85935" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="biocbasics" version="2.12">
         <install version="1.0"> 
             <actions>
                 <action type="set_environment_for_install">
-                      <package name="r3" toolshed="http://testtoolshed.g2.bx.psu.edu" version="3.0.1">
-                            <repository name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-                        </package>
-                    
+                 <package name="r3" toolshed="http://testtoolshed.g2.bx.psu.edu" version="3.0.1">
+                 <repository name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+                 </package>
                 </action>
                 <action type="shell_command">$R_HOME/R CMD BATCH installBioC.R </action>
             </actions>
diff -r 552607114655 -r db24a3130845 rgedgeR/tool_dependencies.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgedgeR/tool_dependencies.xml~	Wed Jun 12 19:58:03 2013 -0400
@@ -0,0 +1,22 @@
+<?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>