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

diff --combined extra/ucsc_encode_submission/ucsc_gather.py
index 1c0759fdf8c5542402501302c060ad16b753a068,07bea2c495b9d2d02309ec270cc7a9f1b0f3c1f0..90b4b3568b360ab120ad74c02c210cd5cbba822b
--- 1/extra/ucsc_encode_submission/ucsc_gather.py
--- 2/extra/ucsc_encode_submission/ucsc_gather.py
+++ b/extra/ucsc_encode_submission/ucsc_gather.py
@@@ -37,7 -37,10 +37,7 @@@ def main(cmdline=None)
      else:
          logging.basicConfig(level = logging.WARNING )        
      
 -    apidata = {'apiid': opts.apiid, 'apikey': opts.apikey }
 -
 -    if opts.host is None or opts.apiid is None or opts.apikey is None:
 -        parser.error("Please specify host url, apiid, apikey")
 +    apidata = api.make_auth_from_opts(opts, parser)
  
      if opts.makeddf and opts.daf is None:
          parser.error("Please specify your daf when making ddf files")
@@@ -70,6 -73,22 +70,6 @@@
  
  
  def make_parser():
 -    # Load defaults from the config files
 -    config = SafeConfigParser()
 -    config.read([os.path.expanduser('~/.htsworkflow.ini'), '/etc/htsworkflow.ini'])
 -    
 -    sequence_archive = None
 -    apiid = None
 -    apikey = None
 -    apihost = None
 -    SECTION = 'sequence_archive'
 -    if config.has_section(SECTION):
 -        sequence_archive = config.get(SECTION, 'sequence_archive',sequence_archive)
 -        sequence_archive = os.path.expanduser(sequence_archive)
 -        apiid = config.get(SECTION, 'apiid', apiid)
 -        apikey = config.get(SECTION, 'apikey', apikey)
 -        apihost = config.get(SECTION, 'host', apihost)
 -
      parser = OptionParser()
  
      # commands
@@@ -89,14 -108,20 +89,14 @@@
      parser.add_option('--force', default=False, action="store_true",
                        help="Force regenerating fastqs")
  
 -    # configuration options
 -    parser.add_option('--apiid', default=apiid, help="Specify API ID")
 -    parser.add_option('--apikey', default=apikey, help="Specify API KEY")
 -    parser.add_option('--host',  default=apihost,
 -                      help="specify HTSWorkflow host",)
 -    parser.add_option('--sequence', default=sequence_archive,
 -                      help="sequence repository")
 -
      # debugging
      parser.add_option('--verbose', default=False, action="store_true",
                        help='verbose logging')
      parser.add_option('--debug', default=False, action="store_true",
                        help='debug logging')
  
 +    api.add_auth_options(parser)
 +    
      return parser
  
  
@@@ -638,9 -663,19 +638,19 @@@ class NameToViewMap(object)
              ('*.condor',                None),
              ('*.daf',                   None),
              ('*.ddf',                   None),
+ 
+             ('*ufflinks?0.9.3.genes.gtf',       'GeneDeNovo'),
+             ('*ufflinks?0.9.3.transcripts.gtf', 'TranscriptDeNovo'),
+             ('*GENCODE-v3c.exonFPKM.gtf',        'ExonsGencV3c'),
+             ('*GENCODE-v3c.genes.gtf',           'GeneGencV3c'),
+             ('*GENCODE-v3c.transcripts.gtf',     'TranscriptGencV3c'),
+             ('*GENCODE-v3c.TSS.gtf',             'TSS'),
+             ('*.junctions.bed6+3',                'Junctions'),
+             
              ('*.?ufflinks-0.9.0?genes.expr',       'GeneDeNovo'),
              ('*.?ufflinks-0.9.0?transcripts.expr', 'TranscriptDeNovo'),
              ('*.?ufflinks-0.9.0?transcripts.gtf',  'GeneModel'),
+ 
              ('*.GENCODE-v3c?genes.expr',       'GeneGCV3c'),
              ('*.GENCODE-v3c?transcript*.expr', 'TranscriptGCV3c'),
              ('*.GENCODE-v3c?transcript*.gtf',  'TranscriptGencV3c'),
@@@ -661,6 -696,7 +671,7 @@@
              ('*.srf',                   None),
              ('*.wig',                   None),
              ('*.zip',                   None),
+             ('transfer_log',            None),
              ]
  
          self.views = {
@@@ -676,6 -712,9 +687,9 @@@
              "GeneModel": {"MapAlgorithm": ma},
              "GeneDeNovo": {"MapAlgorithm": ma},
              "TranscriptDeNovo": {"MapAlgorithm": ma},
+             "ExonsGencV3c": {"MapAlgorithm": ma},
+             "GeneGencV3c": {"MapAlgorithm": ma},
+             "TSS": {"MapAlgorithm": ma},
              "GeneGCV3c": {"MapAlgorithm": ma},
              "TranscriptGCV3c": {"MapAlgorithm": ma},
              "TranscriptGencV3c": {"MapAlgorithm": ma},