Mercurial > repos > iracooke > omssa

changeset 5:3aafd0a91830

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Dependency tweaks
author Ira Cooke <iracooke@gmail.com>
date Fri, 25 Oct 2013 15:19:29 +1100
parents 927cc9160762
children 42b0c5c270f9
files omssa.xml repository_dependencies.xml tool_dependencies.xml
diffstat 3 files changed, 23 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/omssa.xml	Thu Sep 26 14:48:27 2013 +1000
+++ b/omssa.xml	Fri Oct 25 15:19:29 2013 +1100
@@ -1,8 +1,10 @@
 <tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.1">
 
    <requirements>
-	    <requirement type="package" version="2.1.9">protk_omssa</requirement>
-	</requirements>
+	    <requirement type="package" version="1.2.4">protk</requirement>
+    	<requirement type="package" version="2.1.9">omssa</requirement>
+    	<requirement type="package" version="2.2.27">blast+</requirement>
+   </requirements>
 
 
 	<description>Run an OMSSA MS/MS Search</description>
--- a/repository_dependencies.xml	Thu Sep 26 14:48:27 2013 +1000
+++ b/repository_dependencies.xml	Fri Oct 25 15:19:29 2013 +1100
@@ -1,4 +1,10 @@
 <?xml version="1.0"?>
-<repositories description="Proteomics datatypes">
+<repositories description="Proteomics datatypes, omssa and blast executables">
+
 	<repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="7101f7e4b00b"/>
+	<repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_protk_1_2_4" owner="bgruening" changeset_revision="e129907310c2"/>
+	<repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_omssa_2_1_9" owner="iracooke" changeset_revision="a71ce3af685a"/>
+	<repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_blast_plus_2_2_27" owner="iuc" changeset_revision="eab09bc4d63e"/>
+
+
 </repositories>
--- a/tool_dependencies.xml	Thu Sep 26 14:48:27 2013 +1000
+++ b/tool_dependencies.xml	Fri Oct 25 15:19:29 2013 +1100
@@ -1,16 +1,15 @@
 <?xml version="1.0"?>
 <tool_dependency>
-	<package name="protk_omssa" version="2.1.9">
-		<install version="1.0">
-    	<actions>
-     		<action type="setup_rvm" ruby="1.9.3-p448">
-     			<gem version="1.2.4">protk</gem>
-     		</action>
- 			<action type="shell_command">protk_setup.rb blast</action>
- 			<action type="shell_command">protk_setup.rb omssa</action>
-		</actions>
-    	</install>
- 	
- 	<readme>Installer for omssa using the protk ruby gem</readme>
- 	</package>
+	<package name="omssa" version="2.1.9">
+         <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_omssa_2_1_9" owner="iracooke" changeset_revision="a71ce3af685a"/>
+    </package>
+    
+	<package name="protk" version="1.2.4">
+		<repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_protk_1_2_4" owner="bgruening" changeset_revision="e129907310c2"/>
+    </package>
+
+    <package name="blast+" version="2.2.27">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_blast_plus_2_2_27" owner="iuc" changeset_revision="eab09bc4d63e"/>
+    </package>
+
 </tool_dependency>