8 from htsworkflow.pipelines import runfolder
9 from htsworkflow.pipelines.srf import make_srf_commands, make_qseq_commands, \
10 run_commands, pathname_to_run_name
11 from htsworkflow.pipelines.srf import ILLUMINA2SRF10, ILLUMINA2SRF11, SOLEXA2SRF
14 usage = '%prog: [options] runfolder -l 1,2,3 [runfolder -l 5,6 ...]'
16 parser = optparse.OptionParser(usage)
17 parser.add_option('--dry-run', action='store_true',
18 help='print what would be done',
21 parser.add_option('-d', '--dest-dir', dest='dest_dir',
22 help='location to write srf files to',
24 parser.add_option('-s', '--site',
27 parser.add_option('-l', '--lanes', dest='lanes', action="append",
29 help='comma seperated list of lanes to add to srf'
31 parser.add_option('-j', '--jobs', default=1, type='int',
32 help='how many jobs to run simultaneously')
33 parser.add_option('-r', '--runfolder-version', default=ILLUMINA2SRF11, type='int',
34 help='Which class of srf file should we attempt to create\n'
35 '0 = Solexa pipeline 0.2.6 - 0.3\n'
36 '1 = illumina pipeline 1.0\n'
37 '2 = illumina pipeline 1.1rc1 and later \n')
39 parser.add_option('-v', '--verbose', dest='verbose',
40 default=False, action='store_true',
41 help='report more about internals (INFO)')
42 parser.add_option('--debug', dest='debug',
43 default=False, action='store_true',
44 help='report even more about internals (DEBUG)')
48 def parse_lane_arg(lane_arg):
50 Convert comma sperated list of lane ids to a list of integers
53 for lane in lane_arg.split(','):
56 if lane < 1 or lane > 8:
57 parser.error('Lanes must be in range [1..8]')
60 parser.error('Lane selections must be integers')
63 def main(cmdline=None):
64 parser = make_parser()
65 opts, args = parser.parse_args(cmdline)
68 logging.basicConfig(level=logging.DEBUG)
70 logging.basicConfig(level=logging.INFO)
72 logging.basicConfig(level=logging.WARNING)
75 parser.error('need runfolder arguments')
77 # parse lane arguemnts
79 if len(opts.lanes) == 0:
80 lanes_list = [[1,2,3,4,5,6,7,8]] * len(args)
81 elif len(opts.lanes) == len(args):
82 for lane_arg in opts.lanes:
83 lanes_list.append(parse_lane_arg(lane_arg))
86 "Number of lane arguments must match number of runfolders"
89 make_commands = make_qseq_commands
90 # build list of commands
92 for runfolder_path, lanes in zip(args, lanes_list):
93 # normalize paths, either relative to home dirs or current dir
94 runfolder_path = os.path.abspath(runfolder_path)
95 run_name = pathname_to_run_name(runfolder_path)
96 # so any bustard directories?
97 runs = runfolder.get_runs(runfolder_path)
98 # give up if there are anything other than 1 run
100 print 'ERROR: Too many run directories in %s' %(runfolder_path,)
103 bustard_dir = runs[0].bustard.pathname
104 cmds[bustard_dir] = make_commands(run_name,
109 opts.runfolder_version)
111 print "ERROR: Couldn't find a bustard directory in", runfolder_path
115 for cwd, cmd_list in cmds.items():
116 run_commands(cwd, cmd_list, opts.jobs)
118 for cwd, cmd_list in cmds.items():
121 print 'jobs: ', opts.jobs
125 if __name__ == "__main__":
126 sys.exit(main(sys.argv[1:]))