Changeset 2568


Ignore:
Timestamp:
Aug 11, 2014, 10:55:47 AM (7 years ago)
Author:
Nicklas Nordborg
Message:

References #593: Start masking and alignment

Changes related to [2566] to ensure that paths to data files are correct.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/MaskAlignServlet.java

    r2560 r2568  
    323323          Extract lib = merged.getExtract();
    324324          int ca_size = ((Number)Annotationtype.CA_SIZE.getAnnotationValue(dc, lib)).intValue();
    325           // Project name is name of directory in the fastQfolder
    326           String projectName = fastQFolder.substring(0, fastQFolder.indexOf("/"));
    327325             
    328326          MergedSequences ms = MergedSequences.getById(dc, merged.getId());
     
    387385          script.comment("Copy FASTQ files to tmp folder");
    388386          script.progress(10, "Copying FASTQ files");
    389           script.cmd("if [ ! -d \""+projectRoot + "/" + fastQFolder+"\" ]; then");
     387          script.cmd("if [ ! -d \""+projectRoot + fastQFolder+"\" ]; then");
    390388          script.cmd("echo \"Can't find data folder "+fastQFolder+" in " + projectRoot + "\" 1>&2");
    391389          script.cmd("exit 1");
    392390          script.cmd("fi");
    393391          script.cmd("mkdir fastq");
    394           script.cmd("cp " + projectRoot + "/" + fastQFolder + "/*.fastq.gz fastq");
     392          script.cmd("cp " + projectRoot + fastQFolder + "/*.fastq.gz fastq");
    395393          script.newLine();
    396394
     
    458456         
    459457          script.progress(90, "Copying result files to project archive");
    460           script.cmd("mkdir -p " + projectRoot + "/" + tophatFolder);
     458          script.cmd("mkdir -p " + projectRoot + tophatFolder);
    461459          script.cmd("cp fastq.masked/*.out " + jobFolder);
    462460          script.cmd("cp fastq.masked.tophat/*.out " + jobFolder);
    463           script.cmd("cp fastq.masked/*.out " + projectRoot + "/" + tophatFolder);
    464           script.cmd("cp fastq.masked.tophat/* " + projectRoot + "/" + tophatFolder);
     461          script.cmd("cp fastq.masked/*.out " + projectRoot + tophatFolder);
     462          script.cmd("cp fastq.masked.tophat/* " + projectRoot + tophatFolder);
    465463          script.newLine();
    466464         
     
    496494          StringParameterType sType = new StringParameterType();
    497495          alignJob.setParameterValue("jobName", sType, jobName);
    498           alignJob.setParameterValue("jobFolder", sType, jobFolder);
    499           alignJob.setParameterValue("tmpFolder", sType, tmpFolder);
    500496          if (debug)
    501497          {
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