Mercurial > repos > iracooke > tpp_prophets

changeset 7:3f0cb90824f1

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Uploaded
author iracooke
date Tue, 05 Mar 2013 00:28:22 -0500
parents 7005346b534d
children d19a95abf2e4
files README interprophet.xml interprophet_wrapper.rb peptide_prophet.xml peptide_prophet_wrapper.rb pepxml_to_table.xml protein_prophet.xml protein_prophet_wrapper.rb repository_dependencies.xml tool_dependencies.xml
diffstat 10 files changed, 22 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Tue Mar 05 00:28:22 2013 -0500
@@ -0,0 +1,5 @@
+This package installs wrapper scripts for Peptide Prophet, iProphet and Protein Prophet
+
+Requirements:
+This package depends on the galaxy_protk and protk_trans_proteomic_pipeline packages
+Please see instructions for those packages before installing
--- a/interprophet.xml	Mon Mar 04 19:20:05 2013 -0500
+++ b/interprophet.xml	Tue Mar 05 00:28:22 2013 -0500
@@ -1,7 +1,7 @@
-<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.0">
+<tool id="proteomics_search_interprophet_1" name="InterProphet" 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="4.6.1">trans_proteomic_pipeline</requirement>
    </requirements>
 
--- a/interprophet_wrapper.rb	Mon Mar 04 19:20:05 2013 -0500
+++ b/interprophet_wrapper.rb	Tue Mar 05 00:28:22 2013 -0500
@@ -34,7 +34,7 @@
   actual_input_path_string
 end
 
-cmd << "rvm 1.9.3@protk-1.1.9 do interprophet.rb"
+cmd << "rvm 1.9.3@protk-1.2.0 do interprophet.rb"
 
 cmd << " --no-nss" unless use_nss=="blank"
 cmd << " --no-nrs" unless use_nrs=="blank"
--- a/peptide_prophet.xml	Mon Mar 04 19:20:05 2013 -0500
+++ b/peptide_prophet.xml	Tue Mar 05 00:28:22 2013 -0500
@@ -1,6 +1,6 @@
-<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.0.0">
+<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" 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="4.6.1">trans_proteomic_pipeline</requirement>
    </requirements>
    
--- a/peptide_prophet_wrapper.rb	Mon Mar 04 19:20:05 2013 -0500
+++ b/peptide_prophet_wrapper.rb	Tue Mar 05 00:28:22 2013 -0500
@@ -18,7 +18,7 @@
 
 cmd = "ln -s #{original_input_file} #{actual_input_path_string};"
 
-cmd << "rvm 1.9.3@protk-1.1.9 do peptide_prophet.rb"
+cmd << "rvm 1.9.3@protk-1.2.0 do peptide_prophet.rb"
 
 
 ARGV[0]="#{actual_input_path_string}"
--- a/pepxml_to_table.xml	Mon Mar 04 19:20:05 2013 -0500
+++ b/pepxml_to_table.xml	Tue Mar 05 00:28:22 2013 -0500
@@ -1,7 +1,7 @@
-<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.0.0">
+<tool id="pepxml_to_table_1" name="PepXML to Table" 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>
    </requirements>
 
 
@@ -10,7 +10,7 @@
 
 
 <!-- Note .. the input file is assumed to be the first argument -->
-<command>rvm 1.9.3@protk-1.1.9 do pepxml_to_table.rb $input_file -o $output</command>
+<command>rvm 1.9.3@protk-1.2.0 do pepxml_to_table.rb $input_file -o $output</command>
 
 
 <inputs>
--- a/protein_prophet.xml	Mon Mar 04 19:20:05 2013 -0500
+++ b/protein_prophet.xml	Tue Mar 05 00:28:22 2013 -0500
@@ -1,6 +1,6 @@
-<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.0.0">
+<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" 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="4.6.1">trans_proteomic_pipeline</requirement>
    </requirements>
 
--- a/protein_prophet_wrapper.rb	Mon Mar 04 19:20:05 2013 -0500
+++ b/protein_prophet_wrapper.rb	Tue Mar 05 00:28:22 2013 -0500
@@ -17,7 +17,7 @@
 
 cmd = "ln -s #{original_input_file} #{actual_input_path_string};"
 
-cmd << "rvm 1.9.3@protk-1.1.9 do protein_prophet.rb"
+cmd << "rvm 1.9.3@protk-1.2.0 do protein_prophet.rb"
 
 
 ARGV[0]="#{actual_input_path_string}"
--- a/repository_dependencies.xml	Mon Mar 04 19:20:05 2013 -0500
+++ b/repository_dependencies.xml	Tue Mar 05 00:28:22 2013 -0500
@@ -3,8 +3,8 @@
 
      <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_trans_proteomic_pipeline" owner="iracooke" changeset_revision="f302406a0297"/>
+     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349"/>
 
  </repositories>
--- a/tool_dependencies.xml	Mon Mar 04 19:20:05 2013 -0500
+++ b/tool_dependencies.xml	Tue Mar 05 00:28:22 2013 -0500
@@ -1,12 +1,12 @@
 <?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="trans_proteomic_pipeline" version="4.6.1">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="f302406a0297" />
+        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349" />
     </package>
 
 </tool_dependency>
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