Mercurial > repos > fubar > differential_count_models

changeset 76:2a377f98ab76 draft

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Uploaded
author fubar
date Tue, 25 Feb 2014 23:54:15 -0500
parents 8596080a8326
children 4a2e7a9725b2
files tool_dependencies.xml
diffstat 1 files changed, 7 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Feb 18 05:48:23 2014 -0500
+++ b/tool_dependencies.xml	Tue Feb 25 23:54:15 2014 -0500
@@ -1,24 +1,18 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="ghostscript" version="9.10">
-        <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    <package name="r302" version="3.0.2">
+        <repository changeset_revision="c881f61d208e" name="package_r302" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    </package>
+    <package name="ghostscript" version="9.07">
+        <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="graphicsmagick" version="1.3.18">
         <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
-    <package name="r302" version="3.0.2">
-        <repository changeset_revision="c881f61d208e" name="package_r302" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-    </package>
     <package name="biocbasics" version="2.14">
         <install version="1.0"> 
             <actions>
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu/">
-                        <package name="ghostscript" version="9.10" />
-                    </repository>
-                    <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
-                        <package name="graphicsmagick" version="1.3.18" />
-                    </repository>
                     <repository changeset_revision="c881f61d208e" name="package_r302" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                         <package name="r302" version="3.0.2" />
                     </repository>
@@ -30,7 +24,8 @@
                 <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,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 $INSTALL_DIR/runme.R </action>
+                <action type="shell_command">echo "PATH=$PATH 1&gt;&amp;2"</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 and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs