private void executePipelineJob() {
String[] cmd = null;
try {
// write out tempTemplate
File template = new File(outputDirectory, "pipelineTemplate.xml");
if (IO.writeString(xmlTemplate, template) == false)
Misc.printErrAndExit("Problem writing -> " + template);
// build and execute cmd
cmd =
new String[] {
"java",
"-jar",
"-Xmx2G",
pJar.getCanonicalPath(),
"-props",
completePipelinePropFile.getCanonicalPath(),
template.getCanonicalPath()
};
String stringCmd = Misc.stringArrayToString(cmd, " ");
System.out.println("\nExecuting:\n" + stringCmd);
System.out.println("\nPipelineOutput:");
String[] out = IO.executeViaProcessBuilder(cmd, true);
// check output for possible errors
for (String line : out) {
String lcLine = line.toLowerCase();
// watch out for cases where error is mentioned in a warning output line.
if (lcLine.contains("error") && lcLine.startsWith("warning") == false)
Misc.printErrAndExit(
"\n\nERROR found in Pipeline.jar output, see above. Aborting!\n" + line);
}
} catch (Exception e) {
e.printStackTrace();
Misc.printErrAndExit("ERROR: executing " + Misc.stringArrayToString(cmd, " "));
}
}
/** This method will process each argument and assign new variables */
public void processArgs(String[] args) {
Pattern pat = Pattern.compile("-[a-z]");
System.out.println(
"\n" + IO.fetchUSeqVersion() + " Arguments: " + Misc.stringArrayToString(args, " ") + "\n");
for (int i = 0; i < args.length; i++) {
String lcArg = args[i].toLowerCase();
Matcher mat = pat.matcher(lcArg);
if (mat.matches()) {
char test = args[i].charAt(1);
try {
switch (test) {
case 'o':
jobId = args[++i];
break;
case 's':
sampleId = args[++i];
break;
case 'm':
submitter = args[++i];
break;
case 'y':
analysisType = args[++i];
break;
case 'w':
webRootForLinks = new File(args[++i]);
break;
case 'e':
snpEffGenome = args[++i];
break;
case 'i':
minimumReadDepth = args[++i];
break;
case 't':
threads = args[++i];
break;
case 'l':
uploadVarsToNGSWeb = true;
break;
case 'j':
pJar = new File(args[++i]);
break;
case 'p':
truncPipePropFile = new File(args[++i]);
break;
case 'q':
bedForCoverageQC = new File(args[++i]);
break;
case 'b':
bedForVarCalling = new File(args[++i]);
break;
case 'r':
fastaReference = new File(args[++i]);
break;
case 'u':
unfilteredBam = new File(args[++i]);
break;
case 'f':
finalBam = new File(args[++i]);
break;
case 'v':
finalVcf = new File(args[++i]);
break;
case 'd':
outputDirectory = new File(args[++i]);
break;
case 'c':
referenceDir = new File(args[++i]);
break;
case 'h':
printDocs();
System.exit(0);
default:
Misc.printErrAndExit("\nProblem, unknown option! " + mat.group());
}
} catch (Exception e) {
Misc.printErrAndExit(
"\nSorry, something doesn't look right with this parameter: -" + test + "\n");
}
}
}
// check output dir and if needed set sampleId
if (outputDirectory != null) {
outputDirectory.mkdirs();
if (sampleId.length() == 0) sampleId = outputDirectory.getName();
}
// check root directory if needed
if (webRootForLinks != null) {
if (webRootForLinks.exists() == false) webRootForLinks.mkdirs();
// links dir?
File links = new File(webRootForLinks, "links");
if (links.exists() == false) links.mkdirs();
}
// look for required fields and files
checkPrintFields();
checkPrintFiles();
checkForGzippedVcf();
}