def _add_remote_resources(resources):
"""Retrieve remote resources like GATK/MuTect jars present in S3.
"""
out = copy.deepcopy(resources)
for prog, info in resources.iteritems():
for key, val in info.iteritems():
if key == "jar" and objectstore.is_remote(val):
store_dir = utils.safe_makedir(os.path.join(os.getcwd(), "inputs", "jars", prog))
fname = objectstore.download(val, store_dir, store_dir)
version_file = os.path.join(store_dir, "version.txt")
if not utils.file_exists(version_file):
version = install.get_gatk_jar_version(prog, fname)
with open(version_file, "w") as out_handle:
out_handle.write(version)
else:
with open(version_file) as in_handle:
version = in_handle.read().strip()
del out[prog][key]
out[prog]["dir"] = store_dir
out[prog]["version"] = version
return out
def _add_remote_resources(resources):
"""Retrieve remote resources like GATK/MuTect jars present in S3.
"""
out = copy.deepcopy(resources)
for prog, info in resources.items():
for key, val in info.items():
if key == "jar" and objectstore.is_remote(val):
store_dir = utils.safe_makedir(os.path.join(os.getcwd(), "inputs", "jars", prog))
fname = objectstore.download(val, store_dir, store_dir)
version_file = os.path.join(store_dir, "version.txt")
if not utils.file_exists(version_file):
version = install.get_gatk_jar_version(prog, fname)
with open(version_file, "w") as out_handle:
out_handle.write(version)
else:
with open(version_file) as in_handle:
version = in_handle.read().strip()
del out[prog][key]
out[prog]["dir"] = store_dir
out[prog]["version"] = version
return out
