Changeset 2538


Ignore:
Timestamp:
Jul 2, 2014, 2:31:24 PM (7 years ago)
Author:
Nicklas Nordborg
Message:

References #614: Improve error handling when executing jobs on the cluster

Use the new wrapper script for trimmomatic. See http://baseplugins.thep.lu.se/browser/other/pipeline/trunk/stdwrap.sh

File:
1 edited

Legend:

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  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/DemuxMergeServlet.java

    r2497 r2538  
    446446            script.cmd("cp ${ScriptDir}/picard .");
    447447            script.cmd("cp ${ScriptDir}/trimmomatic .");
     448            script.cmd("cp ${ScriptDir}/stdwrap.sh .");
    448449            script.newLine();
    449450          }
     
    707708            script.progress(percent, "Trimmomatic: " + merged.getName());
    708709            script.cmd("echo [" + merged.getName() + "] >> " + trimmomaticOut);
    709             String trimCmd = "./trimmomatic PE";
     710            String trimCmd = "./stdwrap.sh ./trimmomatic PE";
    710711            //trimCmd += " -trimlog fastq.trimmomatic/" + merged.getName()+".log";
    711712            trimCmd += " fastq.merged/"+R1_name;
     
    720721              trimCmd += " " + trim_options;
    721722            }
    722             trimCmd += " >> "+trimmomaticOut+" 2>&1";
     723            trimCmd += " >> "+trimmomaticOut;
    723724            script.cmd(trimCmd);
    724725            script.newLine();
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