diff tool_dependencies.xml @ 39:a793ffd0cd04 draft

Uploaded

--- a/tool_dependencies.xml	Fri Oct 10 11:28:57 2014 -0400
+++ b/tool_dependencies.xml	Tue Dec 23 11:26:33 2014 -0500
@@ -1,13 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
     
-    <!-- PACKAGES -->
     <package name="R" version="3.1.0">
         <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 
     
@@ -16,30 +15,9 @@
     </package>
     
     <!--
-    <package name="snpeff" version="3.4">
-        <repository name="package_snpeff_3_4" owner="jjohnson" prior_installation_required="TRUE" />
-        <readme>Let's see where this msg appears...snpeff</readme>
-    </package>
-    <package name="varscan" version="2">
-        <repository name="varscan_version_2" owner="devteam" prior_installation_required="TRUE" />
-        <readme>Let's see where this msg appears...varscan</readme>
-    </package>
-    -->
-    
-    <!-- ENV -->
-    
     <set_environment>
         <environment_variable action="set_to" name="TOOL_DIR">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
-    <!--
-    <set_environment>
-        <environment_variable action="set_to" name="JAR_PATH1">$JAVA_JAR_PATH</environment_variable>
-    </set_environment>
-    <set_environment>
-        <environment_variable action="set_to" name="JAR_PATH2">$SNPEFF_JAR_PATH</environment_variable>
-    </set_environment>
     -->
-
-    <!--<environment_variable action="set_to" name="VARSCAN_DIR">$JAVA_JAR_PATH</environment_variable>-->
     
 </tool_dependency>