# HG changeset patch
# User iracooke
# Date 1439322930 14400
# Node ID d298e0b6fd72784ed722ac6fc84a1764ef94c29e
# Parent  76d14dc397ed76be24df017dbd9077d2df051989
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840

diff -r 76d14dc397ed -r d298e0b6fd72 peptide_shaker.xml
--- a/peptide_shaker.xml	Tue Jun 16 23:43:15 2015 -0400
+++ b/peptide_shaker.xml	Tue Aug 11 15:55:30 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
diff -r 76d14dc397ed -r d298e0b6fd72 searchgui.xml
--- a/searchgui.xml	Tue Jun 16 23:43:15 2015 -0400
+++ b/searchgui.xml	Tue Aug 11 15:55:30 2015 -0400
@@ -20,6 +20,11 @@
         mkdir output;
         mkdir output_reports;
         cwd=`pwd`;
+        export HOME=\$cwd;
+
+        cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin;
+        tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`;
+
         #for $mgf in $peak_lists:
             #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
             ln -s -f '${mgf}' '${input_name}';
@@ -32,7 +37,7 @@
         ###########################################
         #if $create_decoy:
             echo "Creating decoy database.";
-            java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy &&
+            java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy &&
             rm input_database.fasta &&
             cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
             ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
@@ -42,7 +47,7 @@
         ## generate IdentificationParameters for SearchGUI ##
         #####################################################
 
-        (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI
+        (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI
             -out SEARCHGUI_IdentificationParameters.parameters
 
             @GENERAL_PARAMETERS@
@@ -247,7 +252,7 @@
         ################
         ## Search CLI ##
         ################
-        (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI 
+        (java -Djava.awt.headless=true -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.SearchCLI 
             -temp_folder `pwd`
             -spectrum_files \$cwd
             -output_folder \$cwd/output