# HG changeset patch
# User bgruening
# Date 1380554124 14400
# Node ID 72613128bd65405ff2640b21a36b0c15d1abf68b
# Parent  a05999fd6e268bc20fb05441f25e8520bdc2d831
Uploaded

diff -r a05999fd6e26 -r 72613128bd65 deseq2.xml
--- a/deseq2.xml	Mon Sep 30 10:51:41 2013 -0400
+++ b/deseq2.xml	Mon Sep 30 11:15:24 2013 -0400
@@ -4,7 +4,8 @@
         <requirement type="binary">Rscript</requirement>
         <requirement type="R-module">DESeq2</requirement>
         <requirement type="package" version="3.0.1">R_3_0_1</requirement>
-        <requirement type="set_environment">DESEQ2_SCRIPT_PATH</requirement>
+        <requirement type="package" version="1.0.17">deseq2</requirement>
+        <!--<requirement type="set_environment">DESEQ2_SCRIPT_PATH</requirement>-->
     </requirements>
     <command interpreter="Rscript">
         #import simplejson
@@ -20,7 +21,7 @@
 
             #set $temp_factor_name = list()
             #for $factor in $rep_factorName:
-                #set $temp_factor = dict()                
+                #set $temp_factor = dict()
                 #for $level in $factor.rep_factorLevel:
                     ##$temp_factor_list.append( '%s::%s:%s' % ($factor.factorName.replace(' ','_'), $level.factorLevel, $level.factorIndex) )
                     $temp_factor.update({str($level.factorLevel): map(int, str($level.factorIndex).split(','))})
diff -r a05999fd6e26 -r 72613128bd65 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Sep 30 10:51:41 2013 -0400
+++ b/tool_dependencies.xml	Mon Sep 30 11:15:24 2013 -0400
@@ -6,7 +6,7 @@
     <package name="deseq2" version="1.0.17">
         <repository changeset_revision="3e3d1a50a347" name="package_deseq2_1_0_17" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <set_environment version="1.0">
-        <environment_variable action="set_to" name="DESEQ2_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR/scripts</environment_variable>
-    </set_environment>
+    <!--<set_environment version="1.0">
+        <environment_variable name="DESEQ2_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR/scripts</environment_variable>
+    </set_environment>-->
 </tool_dependency>