diff peptide_shaker.xml @ 6:f62545ff7fa0 draft

Uploaded

--- 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>