# HG changeset patch
# User fubar
# Date 1374898626 14400
# Node ID df4fea3be1b3d9016b33c6e1ccc57974b4b1f88a
# Parent  2122e630b13aedc43ced5f83c11988903db28ea6
Uploaded

diff -r 2122e630b13a -r df4fea3be1b3 rgedgeR/rgedgeRpaired.xml
--- a/rgedgeR/rgedgeRpaired.xml	Fri Jul 26 23:50:59 2013 -0400
+++ b/rgedgeR/rgedgeRpaired.xml	Sat Jul 27 00:17:06 2013 -0400
@@ -3,6 +3,8 @@
   <requirements>
       <requirement type="package" version="2.12">biocbasics</requirement>
       <requirement type="package" version="3.0.1">r3</requirement>
+      <requirement type="package" version="1.3">graphicsmagic</requirement>
+      <requirement type="package" version="9.07">ghostscript</requirement>
   </requirements>
   
   <command interpreter="python">
diff -r 2122e630b13a -r df4fea3be1b3 rgedgeR/tool_dependencies.xml
--- a/rgedgeR/tool_dependencies.xml	Fri Jul 26 23:50:59 2013 -0400
+++ b/rgedgeR/tool_dependencies.xml	Sat Jul 27 00:17:06 2013 -0400
@@ -2,6 +2,12 @@
 <tool_dependency>
     <package name="r3" version="3.0.1">
         <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    </package>package_ghostscript_9_07
+    <package name="ghostscript" version="9.07">
+        <repository changeset_revision="0cdd8d3ffebc" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    </package>
+    <package name="graphicsmagick" version="1.3">
+        <repository changeset_revision="50d546dfd6b9" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="biocbasics" version="2.12">
         <install version="1.0"> 
@@ -16,13 +22,14 @@
                 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" &gt;&gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T)" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos="http://cran.us.r-project.org")" &gt;&gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>                
                 <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
             </actions>
         </install>
-        <readme>Installs some basic bioc packages for the edgeR wrapper 
-        It's clunky but this is the only way I could get anything installed into the package_r3 R
+        <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs
+        It's clunky but this is the most convenient way I could get anything installed into the package_r3
+        Note we use cran at fred hutch since no fastest mirror thingy
        </readme>
     </package>
 </tool_dependency>