X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=scripts%2Fhtsw-srf;fp=scripts%2Fhtsw-srf;h=bcf835dbfa29c1d3707d0e9e602d5c5882093ce4;hb=aa63dd36b1de178acea25d43d3aaef8716763d3d;hp=0000000000000000000000000000000000000000;hpb=5eba67d1e483b3b9abbb68ec3efdb1ef0e95bf46;p=htsworkflow.git

diff --git a/scripts/htsw-srf b/scripts/htsw-srf
new file mode 100755
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+++ b/scripts/htsw-srf
@@ -0,0 +1,126 @@
+#!/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:]))