diff peptide_shaker.xml @ 22:e3be595c0bf5 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d
author iracooke
date Fri, 07 Aug 2015 06:55:04 -0400
parents dfaea053e32f
children 815f93bb3e1b
line wrap: on
line diff
--- a/peptide_shaker.xml	Tue Jun 16 23:43:39 2015 -0400
+++ b/peptide_shaker.xml	Fri Aug 07 06:55:04 2015 -0400
@@ -16,14 +16,18 @@
         #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
         #set $temp_stderr = "peptideshaker_stderr"
 
+
         mkdir output_reports;
         cwd=`pwd`;
 
+        cp -r "\${PEPTIDESHAKER_JAR_PATH%/*}" bin;
+        tmp_peptideshaker_jar_path=`echo "\$cwd/bin/\${PEPTIDESHAKER_JAR_PATH\#\#/*/}"`;
+
         ln -s '$searchgui_input' searchgui_input.zip &&
         ######################
         ## PeptideShakerCLI ##
         ######################
-        (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI
+        (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.PeptideShakerCLI
             -temp_folder \$cwd/PeptideShakerCLI
             -experiment '$exp_str'
             -sample '$samp_str'
@@ -80,7 +84,7 @@
 
         #if 'mzidentML' in str($outputs).split(','):
             echo "Generating mzIdentML";
-            (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.MzidCLI
+            (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.MzidCLI
                 -in \$cwd/peptideshaker_output.zip
                 -output_file output.mzid
                 -contact_first_name "Proteomics"
@@ -99,7 +103,7 @@
         ## and will not be passed to the command line
         #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):
 
-            (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI
+            (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.ReportCLI
                 -temp_folder \$cwd/ReportCLI
                 -in \$cwd/peptideshaker_output.zip
                 -out_reports \$cwd/output_reports