# HG changeset patch
# User bgruening
# Date 1399188054 14400
# Node ID f62545ff7fa0016d6cd8a3098c2d9c9ed917baa7
# Parent  4b15d68afa6c69d2d4df04ad89f48cf66837d680
Uploaded

diff -r 4b15d68afa6c -r f62545ff7fa0 peptide_shaker.xml
--- a/peptide_shaker.xml	Sat May 03 14:06:01 2014 -0400
+++ b/peptide_shaker.xml	Sun May 04 03:20:54 2014 -0400
@@ -5,7 +5,7 @@
     <requirements>
         <requirement type="package" version="0.28.0">peptide_shaker</requirement>
         <requirement type="package" version="1.18.0">searchgui</requirement>
-        <requirement type="package" version="2.2.29">blast+</requirement>
+        <!--<requirement type="package" version="2.2.29">blast+</requirement>-->
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Job Failed" />
@@ -99,7 +99,7 @@
             ## the tree is generated afterwards in PeptideShaker
             -protein_tree 0
 
-            -makeblastdb_folder \$BLAST_ROOT_DIR
+            ##-makeblastdb_folder \$BLAST_ROOT_DIR
 
             #if $advanced.advanced_type_selector == "advanced":
 
@@ -218,9 +218,6 @@
             #end if
         ;
 
-        rm /home/bag/test/foo/* -rf ;
-        cp -R \$cwd /home/bag/test/foo/ ;
-
         #if '0' in str($outputs).split(','):
             find \$cwd/output_reports -name '*Certificate*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
             ;
@@ -242,7 +239,6 @@
             ;
         #end if
 
-        ##cd ..;
         ## the following line is needed. Otherwise, Galaxy will strip away the ';'
         echo 'Finished!';
     </command>
diff -r 4b15d68afa6c -r f62545ff7fa0 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat May 03 14:06:01 2014 -0400
+++ b/tool_dependencies.xml	Sun May 04 03:20:54 2014 -0400
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="searchgui" version="1.18.0">
-        <repository changeset_revision="ee938eef1013" name="package_searchgui_1_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="043d01ef3840" name="package_searchgui_1_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="peptide_shaker" version="0.28.0">
         <repository changeset_revision="dc40b31c1d5b" name="package_peptideshaker_0_28" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="blast+" version="2.2.29">
-        <repository changeset_revision="e78bbab7933d" name="package_blast_plus_2_2_29" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
+    <!--<package name="blast+" version="2.2.29">
+        <repository name="package_blast_plus_2_2_29" owner="iuc" />
+    </package>-->
 </tool_dependency>