from htsworkflow.pipelines.sequences import \
create_sequence_table, \
scan_for_sequences
+from htsworkflow.pipelines import qseq2fastq
+from htsworkflow.pipelines import srf2fastq
def main(cmdline=None):
parser = make_parser()
"""
qseq_condor_header = """
Universe=vanilla
-executable=/woldlab/rattus/lvol0/mus/home/diane/proj/solexa/gaworkflow/scripts/qseq2fastq
+executable=%(exe)s
error=log/qseq2fastq.err.$(process).log
output=log/qseq2fastq.out.$(process).log
log=log/qseq2fastq.log
-"""
+""" % {'exe': sys.executable }
qseq_condor_entries = []
srf_condor_header = """
Universe=vanilla
-executable=/woldlab/rattus/lvol0/mus/home/diane/proj/solexa/gaworkflow/scripts/srf2fastq
+executable=%(exe)s
output=log/srf_pair_fastq.out.$(process).log
error=log/srf_pair_fastq.err.$(process).log
log=log/srf_pair_fastq.log
environment="PYTHONPATH=/home/diane/lib/python2.6/site-packages:/home/diane/proj/solexa/gaworkflow PATH=/woldlab/rattus/lvol0/mus/home/diane/bin:/usr/bin:/bin"
-"""
+""" % {'exe': sys.executable }
srf_condor_entries = []
lib_db = find_archive_sequence_files(host,
apidata,
def condor_srf_to_fastq(srf_file, target_pathname, paired, flowcell=None,
mid=None, force=False):
- args = [ srf_file, ]
+ py = srf2fastq.__file__
+ args = [ py, srf_file, ]
if paired:
args.extend(['--left', target_pathname])
# this is ugly. I did it because I was pregenerating the target
def condor_qseq_to_fastq(qseq_file, target_pathname, flowcell=None, force=False):
- args = ['-i', qseq_file, '-o', target_pathname ]
+ py = qseq2fastq.__file__
+ args = [py, '-i', qseq_file, '-o', target_pathname ]
if flowcell is not None:
args.extend(['-f', flowcell])
script = """