# HG changeset patch
# User Ira Cooke <iracooke@gmail.com>
# Date 1370783812 18000
# Node ID 8f3813e7b0a668f07a1288eec9436ed312a36922
# Parent f77532db59b6ccf3a8318e9515604ba3d61ec769
Update
diff -r f77532db59b6 -r 8f3813e7b0a6 repository_dependencies.xml
--- a/repository_dependencies.xml Tue Mar 05 00:04:49 2013 -0500
+++ b/repository_dependencies.xml Sun Jun 09 08:16:52 2013 -0500
@@ -3,7 +3,6 @@
<repository toolshed="http://10.211.55.28:9009" name="galaxy_protk" owner="iracooke" changeset_revision="2562efef05cb"/>
</repositories>
-->
-
- <repositories description="Requires the protk rubygem to install omssa">
- <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/>
-</repositories>
\ No newline at end of file
+<repositories description="Requires the protk rubygem to install omssa">
+ <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68"/>
+</repositories>
diff -r f77532db59b6 -r 8f3813e7b0a6 tool_dependencies.xml
--- a/tool_dependencies.xml Tue Mar 05 00:04:49 2013 -0500
+++ b/tool_dependencies.xml Sun Jun 09 08:16:52 2013 -0500
@@ -1,10 +1,13 @@
<?xml version="1.0"?>
<tool_dependency>
- <package name="omssa" version="2.1.8">
+ <package name="galaxy_protk" version="1.2.2">
+ <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/>
+ </package>
+ <package name="omssa" version="2.1.9">
<install version="1.0">
<actions>
<action type="download_by_url">https://dl.dropbox.com/u/226794/galaxy_protk.tar.gz</action>
- <action type="shell_command">sh install_omssa.sh $INSTALL_DIR 1.2.0</action>
+ <action type="shell_command">sh install_omssa.sh $INSTALL_DIR 1.2.2</action>
<action type="move_file">
<source>install_omssa.sh</source>
<destination>$INSTALL_DIR</destination>
@@ -17,7 +20,12 @@
</install>
<readme>
Installs OMSSA via the protk installer
+ By default OMSSA will run with as many threads as are available.
+ You can limit the number of threads by setting the environment
+ variable PROTK_OMSSA_NTHREADS to the number of threads you would like OMSSA to use.
+ Please see http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
+ for details on setting environment variables for galaxy tools
</readme>
</package>
-</tool_dependency>
\ No newline at end of file
+</tool_dependency>