def test_load(self):
"""envmod.load function loads specified module
"""
envmod.load('app1')
self.assertEqual(envmod.loaded(), ['app1'])
envmod.load('app2')
self.assertEqual(envmod.loaded(), ['app1', 'app2'])
def test_unload_all(self):
"""envmod.unload_all function unloads all modules
"""
envmod.load('app1', 'app2')
self.assertEqual(envmod.loaded(), ['app1', 'app2'])
envmod.unload_all()
self.assertEqual(envmod.loaded(), [])
def test_load(self):
"""envmod.load function loads specified module
"""
envmod.load('app1')
self.assertEqual(envmod.loaded(),['app1'])
envmod.load('app2')
self.assertEqual(envmod.loaded(),['app1','app2'])
def test_unload_all(self):
"""envmod.unload_all function unloads all modules
"""
envmod.load('app1','app2')
self.assertEqual(envmod.loaded(),['app1','app2'])
envmod.unload_all()
self.assertEqual(envmod.loaded(),[])
def test_unload(self):
"""envmod.unload function unloads specified module
"""
envmod.load('app1', 'app2')
loaded = envmod.loaded()
loaded.sort()
self.assertEqual(loaded, ['app1', 'app2'])
envmod.unload('app1')
loaded = envmod.loaded()
loaded.sort()
self.assertEqual(loaded, ['app2'])
def test_unload(self):
"""envmod.unload function unloads specified module
"""
envmod.load('app1','app2')
loaded = envmod.loaded()
loaded.sort()
self.assertEqual(loaded,['app1','app2'])
envmod.unload('app1')
loaded = envmod.loaded()
loaded.sort()
self.assertEqual(loaded,['app2'])
"(don't execute them)")
args = parser.parse_args()
print "command: %s" % args.command
# Deal with environment modules
if args.command in ("mkfastq", "count", "count-atac"):
modulefiles = args.modulefiles
if modulefiles is None:
try:
modulefiles = __settings.modulefiles['process_10xgenomics']
except KeyError:
# No environment modules specified
pass
if modulefiles is not None:
for modulefile in modulefiles.split(','):
envmod.load(modulefile)
# Check for underlying programs
if args.command == "mkfastq":
required = ["cellranger", "bcl2fastq"]
elif args.command == "count":
required = ["cellranger"]
else:
required = []
for prog in required:
if find_program(prog) is None:
logger.critical("couldn't find '%s'" % prog)
sys.exit(1)
# Run the requested command
if args.command == "mkfastq":
# Set up environment modules
modulefiles = None
try:
modulefiles = options.modulefiles
except AttributeError:
pass
if modulefiles is None:
try:
modulefiles = __settings.modulefiles[cmd]
except KeyError:
# No environment modules specified
pass
if modulefiles is not None:
for modulefile in modulefiles.split(','):
envmod.load(modulefile)
# Setup the processing object and run the requested command
if cmd == 'config':
if options.init:
# Create new settings file and reload
auto_process_ngs.settings.locate_settings_file()
__settings = auto_process_ngs.settings.Settings()
if options.key_value or options.new_section:
if options.new_section is not None:
# Add new sections
for new_section in options.new_section:
try:
new_section = new_section.strip("'").strip('"')
print "Adding section '%s'" % new_section
__settings.add_section(new_section)
