Mercurial > repos > iracooke > omssa

changeset 3:155b6449fdf3

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Uploaded
author iracooke
date Tue, 05 Mar 2013 00:25:34 -0500
parents 5ba3d95534a5
children 54b870eaca8d
files README omssa.xml repository_dependencies.xml tool_dependencies.xml
diffstat 4 files changed, 18 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Tue Mar 05 00:25:34 2013 -0500
@@ -0,0 +1,5 @@
+This package installs wrapper scripts for running OMSSA MS/MS searches
+
+Requirements:
+This package depends on the galaxy_protk, protk_omssa and protk_blast packages
+Please see instructions for those packages before installing
--- a/omssa.xml	Mon Mar 04 18:40:07 2013 -0500
+++ b/omssa.xml	Tue Mar 05 00:25:34 2013 -0500
@@ -1,7 +1,7 @@
-<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.0">
+<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.1">
 
    <requirements>
-	    <requirement type="package" version="1.1.9">galaxy_protk</requirement>
+	    <requirement type="package" version="1.2.0">galaxy_protk</requirement>
     	<requirement type="package" version="2.1.8">omssa</requirement>
     	<requirement type="package" version="2.2.27">blast</requirement>
    </requirements>
@@ -10,8 +10,8 @@
 	<description>Run an OMSSA MS/MS Search</description>
 		
 	<command>#if $database.source_select=="built_in":
-		rvm 1.9.3@protk-1.1.9 do omssa_search.rb -d $database.dbkey 
-		#else #rvm 1.9.3@protk-1.1.9 do omssa_search.rb -d $database.fasta_file
+		rvm 1.9.3@protk-1.2.0 do omssa_search.rb -d $database.dbkey 
+		#else #rvm 1.9.3@protk-1.2.0 do omssa_search.rb -d $database.fasta_file
 		#end if
 		
 		--var-mods='
--- a/repository_dependencies.xml	Mon Mar 04 18:40:07 2013 -0500
+++ b/repository_dependencies.xml	Tue Mar 05 00:25:34 2013 -0500
@@ -6,13 +6,13 @@
 
  
   <repositories description="Proteomics datatypes, omssa and blast executables">
-     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/>
+     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/>
 
-	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="f74290b136fc"/>
+	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="463328a6967f"/>
 
-  	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="88ada6a29993" />
+  	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="0d86d29aaed6" />
 
-    <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="e924c0d646d0" />
+    <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="f77532db59b6" />
 
 
 </repositories>
\ No newline at end of file
--- a/tool_dependencies.xml	Mon Mar 04 18:40:07 2013 -0500
+++ b/tool_dependencies.xml	Tue Mar 05 00:25:34 2013 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <!-- <package name="galaxy_protk" version="1.1.9">
+    <!-- <package name="galaxy_protk" version="1.2.0">
 	     <repository toolshed="http://10.211.55.28:9009" name="galaxy_protk" owner="iracooke" changeset_revision="5610168f3b53"/>
     </package>
 
@@ -12,16 +12,16 @@
         <repository toolshed="http://10.211.55.28:9009" name="protk_omssa" owner="iracooke" changeset_revision="117faa58df2a" />
     </package> -->
 
-<package name="galaxy_protk" version="1.1.9">
-	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/>
+<package name="galaxy_protk" version="1.2.0">
+	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/>
     </package>
 
     <package name="blast" version="2.2.27">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="88ada6a29993" />
+        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="0d86d29aaed6" />
     </package>
 
     <package name="omssa" version="2.1.8">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="e924c0d646d0" />
+        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="f77532db59b6" />
     </package>