def _get_manifest_dir(data=None):
"""
get manifest directory from the data dictionary, falling back on alternatives
it prefers, in order:
1. locating it from the bcbio_system.yaml file
2. locating it from the galaxy directory
3. location it from the python executable.
it can accept either the data or config dictionary
"""
manifest_dir = None
if data:
bcbio_system = tz.get_in(["config", "bcbio_system"], data, None)
bcbio_system = bcbio_system if bcbio_system else data.get(
"bcbio_system", None)
if bcbio_system:
sibling_dir = os.path.normpath(os.path.dirname(bcbio_system))
else:
sibling_dir = dd.get_galaxy_dir(data)
if sibling_dir:
manifest_dir = os.path.normpath(
os.path.join(sibling_dir, os.pardir, "manifest"))
if not manifest_dir or not os.path.exists(manifest_dir):
manifest_dir = os.path.join(config_utils.get_base_installdir(),
"manifest")
return manifest_dir
def _get_manifest_dir(data=None, name=None):
"""
get manifest directory from the data dictionary, falling back on alternatives
it prefers, in order:
1. locating it from the bcbio_system.yaml file
2. locating it from the galaxy directory
3. location it from the python executable.
it can accept either the data or config dictionary
"""
manifest_dir = None
if data:
bcbio_system = tz.get_in(["config", "bcbio_system"], data, None)
bcbio_system = bcbio_system if bcbio_system else data.get("bcbio_system", None)
if bcbio_system:
sibling_dir = os.path.normpath(os.path.dirname(bcbio_system))
else:
sibling_dir = dd.get_galaxy_dir(data)
if sibling_dir:
manifest_dir = os.path.normpath(os.path.join(sibling_dir, os.pardir,
"manifest"))
if not manifest_dir or not os.path.exists(manifest_dir):
manifest_dir = os.path.join(config_utils.get_base_installdir(), "manifest")
if not os.path.exists(manifest_dir) and name:
manifest_dir = os.path.join(config_utils.get_base_installdir(name), "manifest")
return manifest_dir
def get_gemini_dir(data=None):
try:
data_dir = _get_data_dir()
return os.path.join(data_dir, "gemini_data")
except ValueError:
if data:
galaxy_dir = dd.get_galaxy_dir(data)
data_dir = os.path.realpath(os.path.dirname(os.path.dirname(galaxy_dir)))
return os.path.join(data_dir, "gemini_data")
else:
return None
def get_gemini_dir(data=None):
try:
data_dir = _get_data_dir()
return os.path.join(data_dir, "gemini_data")
except ValueError:
if data:
galaxy_dir = dd.get_galaxy_dir(data)
data_dir = os.path.realpath(os.path.dirname(os.path.dirname(galaxy_dir)))
return os.path.join(data_dir, "gemini_data")
else:
return None