# HG changeset patch
# User iracooke
# Date 1362444934 18000
# Node ID 6be01b5359b8db3718f7ce3462c1f41f5c2dd167

Uploaded

diff -r 000000000000 -r 6be01b5359b8 README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Mon Mar 04 19:55:34 2013 -0500
@@ -0,0 +1,15 @@
+This package is an installer for the MSGF+ search tool.
+
+MSGF+ is developed at the Centre for Computational Mass Spectrometry at UCSD. 
+It is described as follows;
+
+Summary
+MS-GF+ is a new MS/MS database search tool that is sensitive (it identifies more peptides than other database search tools and as many peptides as spectral library search tools) and universal (works well for diverse types of spectra, different configurations of MS instruments and different experimental protocols).
+
+MS-GF+ supports the HUPO PSI standard input (mzML) and output (mzIdentML).
+
+
+Full documentation for MSGF+ can be found at these urls
+
+https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355
+http://proteomics.ucsd.edu/Software/MSGFPlus.html#documentation
diff -r 000000000000 -r 6be01b5359b8 repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Mon Mar 04 19:55:34 2013 -0500
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<!-- <repositories description="protk-msgfplus requires the protk rubygem to install MSGF+">
+     <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 MSGF+">
+     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/>
+</repositories>
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diff -r 000000000000 -r 6be01b5359b8 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Mar 04 19:55:34 2013 -0500
@@ -0,0 +1,23 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="msgfplus" version="20130227">
+        <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_msgfplus.sh $INSTALL_DIR 1.1.9</action>
+                <action type="move_file">
+                    <source>install_msgfplus.sh</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PROTK_MSGFPLUS_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Installs MSGF+ via the protk installer
+        </readme>
+    </package>
+
+</tool_dependency>
\ No newline at end of file