Mercurial > repos > stef > falco

diff tool_dependencies.xml @ 25:2210b89487c6 draft

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Uploaded
author stef
date Fri, 10 Oct 2014 06:13:06 -0400
parents e0c2f731d747
children 3419fc808193
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed Oct 08 08:14:41 2014 -0400
+++ b/tool_dependencies.xml	Fri Oct 10 06:13:06 2014 -0400
@@ -2,42 +2,45 @@
 <tool_dependency>
     
     <!-- PACKAGES -->
-    <package name="R" version="3.0.3">
-        <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-        <readme>Let's see where this msg appears...R</readme>
+    <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" />
-        <readme>Let's see where this msg appears...samtools</readme>
     </package>
 
+    <!--
     <package name="bcftools" version="2">
-        <repository changeset_revision="5f9ba601748e" name="bcftools" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository name="bcftools" owner="iuc" prior_installation_required="TRUE" />
         <readme>Let's see where this msg appears...bcftools</readme>
     </package>
     
     <package name="snpeff" version="3.4">
-        <repository changeset_revision="7fb1061d905a" name="package_snpeff_3_4" owner="jjohnson" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <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 changeset_revision="f82940004c84" name="varscan_version_2" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <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>