private void addCommands() throws IOException {
String baseName = FilenameUtils.getBaseName(bam.getAbsolutePath());
File logFile = new File(bam.getParentFile(), baseName + "_qualimap.log");
File tmpDir = new File("/tmp", baseName);
File localQualimapReport = new File(tmpDir, "report.pdf");
String appendAlloutputToLog = " >> " + logFile.getAbsolutePath() + " 2>&1";
// create a tmp dir
addCommand("mkdir " + tmpDir + appendAlloutputToLog);
addCommand("\n");
addCommand(
"unset DISPLAY"); // somehow needed to prevent missing X11 error from qualimap when the
// pipeline is executed from a user not logged in with - X
// call the raw variants
addCommand(
gc.getQualiMap().getAbsolutePath()
+ " bamqc "
+ " -bam "
+ bam.getAbsolutePath()
+ " -outdir "
+ tmpDir.getAbsolutePath()
+ " -outformat PDF"
+ " -nt "
+ gc.getQualimapSGEThreads()
+ " --java-mem-size="
+ gc.getQualimapSGEMemory()
+ "G"
+ appendAlloutputToLog);
addCommand("\n");
// copy the resutls back
addCommand(
"cp "
+ localQualimapReport.getAbsolutePath()
+ " "
+ qualimapReport.getAbsolutePath()
+ appendAlloutputToLog);
addCommand("\n");
// remove the tmp dir from the sge host
addCommand("rm -rf " + tmpDir.getAbsolutePath() + appendAlloutputToLog);
addCommand("\n");
addCommand("echo finished " + appendAlloutputToLog);
addCommand("date " + appendAlloutputToLog);
}
public QualimapJob(File bam, File qualimapReport, GlobalConfiguration gc, String hostNameArg)
throws IOException {
super(FilenameUtils.removeExtension(bam.getAbsolutePath()) + "_qualimap.sh");
this.bam = bam;
this.qualimapReport = qualimapReport;
this.gc = gc;
sgeName = "qualimap_" + bam.getName();
hostName = hostNameArg;
this.sgeThreads = 8;
sgeThreads = gc.getQualimapSGEThreads();
addCommands();
close();
}