import sys
from htsworkflow.pipelines.retrieve_config import *
from htsworkflow.pipelines import retrieve_config
-from htsworkflow.pipelines.genome_mapper import getAvailableGenomes
-from htsworkflow.pipelines.genome_mapper import constructMapperDict
#Turn on built-in command-line parsing.
retrieve_config.DISABLE_CMDLINE = False
-def main(args=None):
- #Display help if no args are presented
- if len(sys.argv) == 1:
- sys.argv.append('-h')
+def main(argv=None):
+ if argv is None:
+ argv = sys.argv
- options = getCombinedOptions()
+ #Display help if no args are presented
+ options = getCombinedOptions(argv)
+
msg_list = ['ERROR MESSAGES:']
- if options.output_filepath is None:
- msg_list.append(" Output filepath argument required. -o <filepath> or --output=<filepath>")
-
if options.flowcell is None:
msg_list.append(" Flow cell argument required. -f <flowcell> or --flowcell=<flowcell>")
print '\n'.join(msg_list)
return 1
- saveConfigFile(options.flowcell, options.url, options.output_filepath)
-
- f = open(options.output_filepath, 'r')
- data = f.read()
- f.close()
-
- genome_dict = getAvailableGenomes(options.genome_dir)
- mapper_dict = constructMapperDict(genome_dict)
-
- f = open(options.output_filepath, 'w')
- f.write(data % (mapper_dict))
- f.close()
+ saveConfigFile(options)
return 0