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
