Mercurial > repos > stef > qdnaseq_test

changeset 14:92d2691d30e5 draft

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Uploaded
author stef
date Thu, 06 Nov 2014 04:22:05 -0500
parents f8b16dd1ecb7
children 233dc7c38b65
files tool_dependencies.xml
diffstat 1 files changed, 12 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Thu Nov 06 04:21:57 2014 -0500
+++ b/tool_dependencies.xml	Thu Nov 06 04:22:05 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" -->
     <!-- 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" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </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>
 
     <!--
-    <package name="qdnaseq" version="1.0.5">
-        <repository name="package_qdnaseq_1_0_5" owner="stef"/>
-    </package>
+    <action type="set_environment">
+        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+    </action>
     -->
-
-    
-    <action type="set_environment">
-        <environment_variable name="INSTALL_DIR" action="prepend_to">$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>