Mercurial > repos > galaxyp > peptideshaker

comparison searchgui.xml @ 23:913dbf2b83e0 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840
author iracooke
date Mon, 10 Aug 2015 18:25:37 -0400
parents e3be595c0bf5
children 815f93bb3e1b
comparison
equal deleted inserted replaced
22:e3be595c0bf5 23:913dbf2b83e0
18 #set $temp_stderr = "searchgui_stderr" 18 #set $temp_stderr = "searchgui_stderr"
19 19
20 mkdir output; 20 mkdir output;
21 mkdir output_reports; 21 mkdir output_reports;
22 cwd=`pwd`; 22 cwd=`pwd`;
23 export HOME=\$cwd;
23 24
24 cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin; 25 cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin;
25 tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`; 26 tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`;
26 27
27 #for $mgf in $peak_lists: 28 #for $mgf in $peak_lists: