Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow

[htsworkflow.git] / scripts / srf

diff --git a/scripts/srf b/scripts/srf
deleted file mode 100755 (executable)
index bcf835d..0000000
--- a/scripts/srf
+++ /dev/null
@@ -1,126 +0,0 @@
-#!/usr/bin/python
-
-import logging
-import optparse
-import os
-import sys
-
-from htsworkflow.pipelines import runfolder
-from htsworkflow.pipelines.srf import make_srf_commands, make_qseq_commands, \
-                                      run_commands, pathname_to_run_name
-from htsworkflow.pipelines.srf import ILLUMINA2SRF10, ILLUMINA2SRF11, SOLEXA2SRF
-
-def make_parser():
-  usage = '%prog: [options] runfolder -l 1,2,3 [runfolder -l 5,6 ...]'
-
-  parser = optparse.OptionParser(usage)
-  parser.add_option('--dry-run', action='store_true',
-                    help='print what would be done',
-                    default=False)
-
-  parser.add_option('-d', '--dest-dir', dest='dest_dir',
-                    help='location to write srf files to',
-                    default='.')
-  parser.add_option('-s', '--site',
-                    help='site name',
-                    default='Individual')
-  parser.add_option('-l', '--lanes', dest='lanes', action="append",
-         default=[],
-         help='comma seperated list of lanes to add to srf'
-  )
-  parser.add_option('-j', '--jobs', default=1, type='int',
-                    help='how many jobs to run simultaneously')
-  parser.add_option('-r', '--runfolder-version', default=ILLUMINA2SRF11, type='int',
-                    help='Which class of srf file should we attempt to create\n'
-                         '0 = Solexa pipeline 0.2.6 - 0.3\n'
-                         '1 = illumina pipeline 1.0\n'
-                         '2 = illumina pipeline 1.1rc1 and later \n')
-                     
-  parser.add_option('-v', '--verbose', dest='verbose',
-                    default=False, action='store_true',
-                    help='report more about internals (INFO)')
-  parser.add_option('--debug', dest='debug',
-                    default=False, action='store_true',
-                    help='report even more about internals (DEBUG)')
- 
-  return parser
-
-def parse_lane_arg(lane_arg):
-    """
-    Convert comma sperated list of lane ids to a list of integers
-    """
-    lanes = []
-    for lane in lane_arg.split(','):
-        try:
-            lane = int(lane)
-            if lane < 1 or lane > 8:
-                parser.error('Lanes must be in range [1..8]')
-            lanes.append(lane)
-        except ValueError:
-            parser.error('Lane selections must be integers')
-    return lanes
-
-def main(cmdline=None):
-    parser = make_parser()
-    opts, args = parser.parse_args(cmdline)
-   
-    if opts.debug: 
-        logging.basicConfig(level=logging.DEBUG)
-    elif opts.verbose:
-        logging.basicConfig(level=logging.INFO)
-    else:
-        logging.basicConfig(level=logging.WARNING)
-
-    if len(args) == 0:
-        parser.error('need runfolder arguments')
-
-    # parse lane arguemnts
-    lanes_list = []
-    if len(opts.lanes) == 0:
-        lanes_list = [[1,2,3,4,5,6,7,8]] * len(args)
-    elif len(opts.lanes) == len(args):
-        for lane_arg in opts.lanes:
-            lanes_list.append(parse_lane_arg(lane_arg))
-    else:
-        parser.error(
-          "Number of lane arguments must match number of runfolders"
-        )
-
-    make_commands = make_qseq_commands
-    # build list of commands
-    cmds = {}
-    for runfolder_path, lanes in zip(args, lanes_list):
-        # normalize paths, either relative to home dirs or current dir
-        runfolder_path = os.path.abspath(runfolder_path)
-        run_name = pathname_to_run_name(runfolder_path)
-        # so any bustard directories?
-        runs = runfolder.get_runs(runfolder_path)
-        # give up if there are anything other than 1 run
-        if len(runs) > 1:
-          print 'ERROR: Too many run directories in %s' %(runfolder_path,)
-          return 1
-        elif len(runs) == 1:
-          bustard_dir = runs[0].bustard.pathname
-          cmds[bustard_dir] = make_commands(run_name,
-                                            bustard_dir,
-                                            lanes,
-                                            opts.site,
-                                            opts.dest_dir,
-                                            opts.runfolder_version)
-        else:
-          print "ERROR: Couldn't find a bustard directory in", runfolder_path
-          return 1
-
-    if not opts.dry_run:
-      for cwd, cmd_list in cmds.items():
-        run_commands(cwd, cmd_list, opts.jobs)
-    else:
-      for cwd, cmd_list in cmds.items():
-        print cwd
-        print cmd_list
-        print 'jobs: ', opts.jobs
-
-    return 0
-
-if __name__ == "__main__":
-    sys.exit(main(sys.argv[1:]))