diff tool_dependencies.xml @ 74:0feb7fa37245 draft

Uploaded

--- a/tool_dependencies.xml	Fri Oct 24 07:06:55 2014 -0400
+++ b/tool_dependencies.xml	Thu Nov 06 05:09:17 2014 -0500
@@ -2,28 +2,27 @@
 <tool_dependency>
     
     <package name="samtools" version="0.1.18">
-        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="TRUE" />
+        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 
-    <!-- As soon as R 3_1_0 package works good, all dependencies will be set via "package_qdnaseq_1_0_5" -->
+    <!-- As soon as R 3_1_0 package works with all packages, all dependencies will be set via "package_qdnaseq_1_0_5" -->
     <!-- Currently these have to be manually installed by installing Bioconductor package "QDNAseq" -->
     
     <!--
     <package name="R" version="3.1.0">
-        <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="TRUE" />
+        <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="TRUE" />
     </package>
     -->
 
     <!--
     <package name="qdnaseq" version="1.0.5">
-        <repository name="package_qdnaseq_1_0_5" owner="stef"/>
+        <repository name="package_qdnaseq_1_0_5" owner="stef" prior_installation_required="TRUE"/>
     </package>
     -->
-
-    <!--
-    <action type="set_environment">
-        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-    </action>
-    -->
+    
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="QDNASEQ_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+    
     
 </tool_dependency>