def run(self): ########################################## #Setup a file tree. ########################################## tempFileTree = TempFileTree(os.path.join(self.getGlobalTempDir(), getRandomAlphaNumericString())) fileTreeRootFile = tempFileTree.getTempFile() makeFileTree(fileTreeRootFile, \ self.depth, tempFileTree) treePointer = tempFileTree.getTempFile() makeTreePointer(fileTreeRootFile, treePointer) logger.info("We've set up the file tree") ########################################## #Issue the child and follow on jobs ########################################## self.addChildTarget(ChildTarget(treePointer)) self.setFollowOnTarget(DestructFileTree(tempFileTree)) logger.info("We've added the child target and finished SetupFileTree.run()")
def run_single_star(target, genome, institute, tissue, reference, out_dir, experiment, fastq_path, num_threads, ref_genome): tmp_dir = os.path.join(target.getLocalTempDir(), "tmp_" + getRandomAlphaNumericString()) out_path = build_out_dirs(out_dir, genome, institute, tissue, experiment) + "/" star_cmd = ['STAR', '--genomeDir', reference, '--readFilesIn', fastq_path, '--outFileNamePrefix', out_path, '--outTmpDir', tmp_dir, '--runThreadN', num_threads] runProc(star_cmd + star_flags) os.remove(fastq_path) target.setFollowOnTargetFn(run_feature_counts, args=(genome, out_path, reference, ref_genome, num_threads, False))
def run_paired_star(target, genome, institute, tissue, reference, out_dir, experiment, fwd_fastq_path, rev_fastq_path, num_threads, ref_genome): # STAR wants a temp dir that doesn't exist, so we have to give it a fresh path because jobTree makes localTempDir() tmp_dir = os.path.join(target.getLocalTempDir(), "tmp_" + getRandomAlphaNumericString()) out_path = build_out_dirs(out_dir, genome, institute, tissue, experiment) + "/" star_cmd = ['STAR', '--genomeDir', reference, '--readFilesIn', fwd_fastq_path, rev_fastq_path, '--outFileNamePrefix', out_path, '--outTmpDir', tmp_dir, '--runThreadN', num_threads] runProc(star_cmd + star_flags) os.remove(fwd_fastq_path) os.remove(rev_fastq_path) target.setFollowOnTargetFn(run_feature_counts, args=(genome, out_path, reference, ref_genome, num_threads, True))
def run_single_star(target, genome, institute, tissue, reference, out_dir, experiment, fastq_path, num_threads, rsem, htseq): tmp_dir = os.path.join(target.getLocalTempDir(), "tmp_" + getRandomAlphaNumericString()) out_path = build_out_dirs(out_dir, genome, institute, tissue, experiment) + "/" star_cmd = ['STAR', '--genomeDir', reference, '--readFilesIn', fastq_path, '--outFileNamePrefix', out_path, '--outTmpDir', tmp_dir, '--runThreadN', num_threads] runProc(star_cmd + star_flags) if rsem is True: target.setFollowOnTargetFn(run_rsem, args=(genome, out_path, reference, False), cpu=1) if htseq is True: target.setFollowOnTargetFn(run_htseq, args=(genome, out_path, reference), cpu=1)
def __init__(self, depth=0): Target.__init__(self, time=random.random() * 10) self.tempFileName = getRandomAlphaNumericString() self.depth = depth