Mercurial > repos > iracooke > msgfplus

changeset 7:b3f2bd49029c

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Uploaded
author iracooke
date Tue, 05 Mar 2013 00:20:42 -0500
parents ce2f26664c9d
children 4f6cbe948065
files README msgfplus_search.xml repository_dependencies.xml tool_dependencies.xml
diffstat 4 files changed, 15 insertions(+), 24 deletions(-) [+]
line wrap: on
line diff
--- a/README	Mon Mar 04 21:44:52 2013 -0500
+++ b/README	Tue Mar 05 00:20:42 2013 -0500
@@ -1,16 +1,7 @@
 This package is a galaxy wrapper for the MSGF+ search tool.
 
-The underlying MSGF+ tool itself should be automatically installed however you must
-satisfy the requirements below before attempting to install.
-
-System Requirements. Ensure that you have the following packages installed on your system
+Requirements:
+This package depends on the galaxy_protk and protk_msgfplus and protk_proteowizard packages
+Please see instructions for those packages before installing
 
-(For protk_msgfplus)
-- unzip
-- java runtime 6 or higher
-
-(For galaxy_protk)
-- The ability to download files (an internet connection): curl wget
-- gcc g++ make autoconf automake libtool pkg-config patch git openssl 
-libreadline6 libreadline6-dev git-core zlib1g zlib1g-dev libssl-dev
-libc6-dev ncurses-dev bison subversion libxml2 libxml2-dev
+In addition to basic requirements you must also have unzip and java 6 runtime (or greater) installed
--- a/msgfplus_search.xml	Mon Mar 04 21:44:52 2013 -0500
+++ b/msgfplus_search.xml	Tue Mar 05 00:20:42 2013 -0500
@@ -1,7 +1,7 @@
-<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.0">
+<tool id="proteomics_search_msgfplus_1" name="MSGF+ 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="20130227">msgfplus</requirement>
     	<requirement type="package" version="3_0_4388">proteowizard</requirement>
    	</requirements>
@@ -11,8 +11,8 @@
 
 	<command>
 		#if $database.source_select=="built_in":
-		rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb --galaxy -d $database.dbkey
-		#else #rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb -d $database.fasta_file
+		rvm 1.9.3@protk-1.2.0 do msgfplus_search.rb --galaxy -d $database.dbkey
+		#else #rvm 1.9.3@protk-1.2.0 do msgfplus_search.rb --galaxy -d $database.fasta_file
 		#end if
 
 		--var-mods='
--- a/repository_dependencies.xml	Mon Mar 04 21:44:52 2013 -0500
+++ b/repository_dependencies.xml	Tue Mar 05 00:20:42 2013 -0500
@@ -3,10 +3,10 @@
 
      <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="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="protk_msgfplus" owner="iracooke" changeset_revision="87757d28e0d2"/>
+     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_msgfplus" owner="iracooke" changeset_revision="21c7f6a61d61"/>
 
-     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_proteowizard" owner="iracooke" changeset_revision="6ead3520e93a"/>
+     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_proteowizard" owner="iracooke" changeset_revision="dd22a794a86b"/>
 
  </repositories>
--- a/tool_dependencies.xml	Mon Mar 04 21:44:52 2013 -0500
+++ b/tool_dependencies.xml	Tue Mar 05 00:20:42 2013 -0500
@@ -1,16 +1,16 @@
 <?xml version="1.0"?>
 <tool_dependency>
 
-    <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="proteowizard" version="3_0_4388">
-	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_proteowizard" owner="iracooke" changeset_revision="6ead3520e93a"/>
+	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_proteowizard" owner="iracooke" changeset_revision="dd22a794a86b"/>
 	</package>
 
     <package name="msgfplus" version="20130227">
-	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_msgfplus" owner="iracooke" changeset_revision="87757d28e0d2"/>
+	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_msgfplus" owner="iracooke" changeset_revision="21c7f6a61d61"/>
     </package>