Mercurial > repos > galaxyp > peptideshaker
diff searchgui.xml @ 12:d298e0b6fd72 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840
| author | iracooke |
|---|---|
| date | Tue, 11 Aug 2015 15:55:30 -0400 |
| parents | 76d14dc397ed |
| children | 3ccfbb673089 |
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--- 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