add_debug_option(p.parser_for('info'))
# Add copy command
p.add_command('copy',help="Copy fastqs from ANALYSIS_DIR",
usage="%prog copy [OPTIONS] ANALYSIS_DIR DEST_DIR",
description="Copy fastqs from ANALYSIS_DIR to DEST_DIR.")
p.parser_for('copy').add_option('--projects',action='store',dest='projects',default=None,
help="Restrict copying to projects matching the "
"supplied pattern")
p.parser_for('copy').add_option('--fastq-dir',action='store',dest='fastq_dir',default=None,
help="Only copy fastqs from the specified FASTQ_DIR")
add_dry_run_option(p.parser_for('copy'))
add_debug_option(p.parser_for('copy'))
# Process the command line
cmd,options,args = p.parse_args()
if len(args) < 1:
p.error("Need to supply a directory to examine")
if options.debug:
logging.getLogger().setLevel(logging.DEBUG)
# Acquire data for putative analysis directory
dirn = os.path.abspath(args[0])
print "Examining %s" % dirn
analysis_dir = utils.AnalysisDir(dirn)
if not (analysis_dir.n_projects and analysis_dir.n_sequencing_data):
logging.warning("Not an analysis directory")
sys.exit()
# Deal with commands
if cmd == 'info':
# Report projects from sequencing data
if analysis_dir.n_sequencing_data:
for data in analysis_dir.sequencing_data:
print "Sequencing data projects found in '%s':\n" % \
else:
# For other options check if an analysis
# directory was specified
if len(args) > 0:
analysis_dir = args[0]
else:
analysis_dir = os.getcwd()
# Turn off allow save for specific commands
if cmd in ('params','metadata','report'):
allow_save = False
# Run the specified stage
d = AutoProcess(analysis_dir,allow_save_params=allow_save)
if cmd == 'make_fastqs':
# Deal with --no-lane-splitting
if options.no_lane_splitting and options.use_lane_splitting:
p.error("--no-lane-splitting and --use-lane-splitting "
"are mutually exclusive")
elif options.no_lane_splitting:
no_lane_splitting = True
elif options.use_lane_splitting:
no_lane_splitting = False
else:
no_lane_splitting = None
# Do the make_fastqs step
d.make_fastqs(skip_rsync=options.skip_rsync,
nprocessors=options.nprocessors,
runner=options.runner,
remove_primary_data=options.remove_primary_data,
ignore_missing_bcl=options.ignore_missing_bcl,
ignore_missing_stats=options.ignore_missing_stats,
generate_stats=(not options.no_stats),
require_bcl2fastq_version=options.bcl2fastq_version,
