diff tool_dependencies.xml @ 23:4943308e95fc draft

Uploaded

--- a/tool_dependencies.xml	Thu Nov 06 05:49:13 2014 -0500
+++ b/tool_dependencies.xml	Wed Mar 04 08:36:24 2015 -0500
@@ -4,22 +4,25 @@
     <package name="samtools" version="0.1.18">
         <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 with all packages, all dependencies will be set via "package_qdnaseq_1_2_2" -->
+    <!-- Currently these have to be manually installed by installing Bioconductor package "QDNAseq" -->
     
-    <package name="R_3_1_1" version="3.1.1">
-        <repository changeset_revision="d9964efbfbe3" name="package_r_3_1_1" owner="fubar" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <!--
+    <package name="R" version="3.1.0">
+        <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 changeset_revision="14491b8d4d2b" name="package_qdnaseq_1_0_5" owner="stef" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
+    -->
 
     <!--
-    <action type="set_environment">
-        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-    </action>
+    <package name="qdnaseq" version="1.2.2">
+        <repository name="package_qdnaseq_1_2_2" owner="stef" prior_installation_required="TRUE"/>
+    </package>
     -->
+    
     <set_environment version="1.0">
         <environment_variable action="set_to" name="QDNASEQ_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
     
+    
 </tool_dependency>