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