def get_post_process_yaml(data_dir, workdir):
try:
from bcbiovm.docker.defaults import get_datadir
datadir = get_datadir()
system = os.path.join(datadir, "galaxy", "bcbio_system.yaml") if datadir else None
except ImportError:
system = None
if system is None or not os.path.exists(system):
try:
_, system = load_system_config("bcbio_system.yaml")
except ValueError:
system = None
sample = os.path.join(data_dir, "post_process-sample.yaml")
std = os.path.join(data_dir, "post_process.yaml")
if os.path.exists(std):
return std
elif system and os.path.exists(system):
# create local config pointing to reduced genomes
test_system = os.path.join(workdir, os.path.basename(system))
with open(system) as in_handle:
config = yaml.load(in_handle)
config["galaxy_config"] = os.path.join(data_dir, "universe_wsgi.ini")
with open(test_system, "w") as out_handle:
yaml.dump(config, out_handle)
return test_system
else:
return sample
def get_post_process_yaml(data_dir, workdir):
try:
from bcbiovm.docker.defaults import get_datadir
datadir = get_datadir()
system = os.path.join(datadir, "galaxy",
"bcbio_system.yaml") if datadir else None
except ImportError:
system = None
if system is None or not os.path.exists(system):
try:
_, system = load_system_config("bcbio_system.yaml")
except ValueError:
system = None
sample = os.path.join(data_dir, "post_process-sample.yaml")
std = os.path.join(data_dir, "post_process.yaml")
if os.path.exists(std):
return std
elif system and os.path.exists(system):
# create local config pointing to reduced genomes
test_system = os.path.join(workdir, os.path.basename(system))
with open(system) as in_handle:
config = yaml.load(in_handle)
config["galaxy_config"] = os.path.join(data_dir,
"universe_wsgi.ini")
with open(test_system, "w") as out_handle:
yaml.dump(config, out_handle)
return test_system
else:
return sample
def get_post_process_yaml(data_dir, workdir):
"""Prepare a bcbio_system YAML file pointing to test data.
"""
try:
from bcbiovm.docker.defaults import get_datadir
datadir = data_dir or get_datadir()
sys_conf_file = os.path.join(datadir, "galaxy", "bcbio_system.yaml")
system = sys_conf_file if datadir else None
except ImportError:
system = None
if system is None or not os.path.exists(system):
try:
_, system = load_system_config(config_file="bcbio_system.yaml",
work_dir=workdir)
except ValueError:
system = None
if system is None or not os.path.exists(system):
system = os.path.join(data_dir, "post_process-sample.yaml")
# create local config pointing to reduced genomes
test_system = os.path.join(workdir, "bcbio_system.yaml")
with open(system) as in_handle:
config = yaml.load(in_handle)
config["galaxy_config"] = os.path.join(data_dir, "universe_wsgi.ini")
with open(test_system, "w") as out_handle:
yaml.dump(config, out_handle)
return test_system
def get_post_process_yaml(data_dir, workdir):
"""Prepare a bcbio_system YAML file pointing to test data.
"""
try:
from bcbiovm.docker.defaults import get_datadir
datadir = data_dir or get_datadir()
sys_conf_file = os.path.join(datadir, "galaxy", "bcbio_system.yaml")
system = sys_conf_file if datadir else None
except ImportError:
system = None
if system is None or not os.path.exists(system):
try:
_, system = load_system_config(config_file="bcbio_system.yaml", work_dir=workdir)
except ValueError:
system = None
if system is None or not os.path.exists(system):
system = os.path.join(data_dir, "post_process-sample.yaml")
# create local config pointing to reduced genomes
test_system = os.path.join(workdir, "bcbio_system.yaml")
with open(system) as in_handle:
config = yaml.load(in_handle)
config["galaxy_config"] = os.path.join(data_dir, "universe_wsgi.ini")
with open(test_system, "w") as out_handle:
yaml.dump(config, out_handle)
return test_system
def _get_bcbiovm_config(data_dir):
try:
from bcbiovm.docker.defaults import get_datadir
datadir = data_dir or get_datadir()
sys_conf_file = os.path.join(datadir, "galaxy", "bcbio_system.yaml")
system = sys_conf_file if datadir else None
except ImportError:
system = None
return system
def _get_bcbiovm_config(data_dir):
try:
from bcbiovm.docker.defaults import get_datadir
datadir = data_dir or get_datadir()
sys_conf_file = os.path.join(datadir, "galaxy", "bcbio_system.yaml")
system = sys_conf_file if datadir else None
except ImportError:
system = None
return system