# HG changeset patch
# User bgruening
# Date 1389949456 18000
# Node ID a8dc71379df077103bb8284d401cc2dee71bc4ad
# Parent  b1b96b6ed60c0b6b87ef4f32caa9b456167bd05a
Uploaded

diff -r b1b96b6ed60c -r a8dc71379df0 diffbind.R
--- a/diffbind.R	Thu Jan 16 04:17:16 2014 -0500
+++ b/diffbind.R	Fri Jan 17 04:04:16 2014 -0500
@@ -27,9 +27,7 @@
     q(status=1);
 }
 
-
 library('DiffBind')
-# used to save to BED, GFF or WIG format
 
 if ( !is.null(opt$plots) ) {
     pdf(opt$plots)
diff -r b1b96b6ed60c -r a8dc71379df0 diffbind.xml
--- a/diffbind.xml	Thu Jan 16 04:17:16 2014 -0500
+++ b/diffbind.xml	Fri Jan 17 04:04:16 2014 -0500
@@ -6,6 +6,7 @@
         <requirement type="package" version="3.0.1">R_3_0_1</requirement>
         <requirement type="package" version="1.0.17">deseq2</requirement>
         <requirement type="package" version="1.8.3">diffbind</requirement>
+        <requirement type="set_environment">DIFFBIND_SCRIPT_PATH</requirement>
     </requirements>
     <command>
         ## seems that diffbind also needs file extensions to work properly
@@ -18,7 +19,7 @@
             #set $counter = $counter + 1
         #end for
 
-        Rscript /usr/local/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/bgruening/diffbind/7929c8b3f6f9/diffbind/diffbind.R
+        Rscript \$AUGUSTUS_SCRIPT_PATH/diffbind.R
             -i $infile
             -o $outfile
             -p $plots
diff -r b1b96b6ed60c -r a8dc71379df0 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jan 16 04:17:16 2014 -0500
+++ b/tool_dependencies.xml	Fri Jan 17 04:04:16 2014 -0500
@@ -4,9 +4,11 @@
         <repository changeset_revision="0a395bcd7efd" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="deseq2" version="1.0.17">
-        <repository changeset_revision="3b6a8c377895" name="package_deseq2_1_0_17" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c62e0a0f4fed" name="package_deseq2_1_0_17" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="DIFFBIND_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
     <package name="diffbind" version="1.8.3">
         <install version="1.0">
             <actions>