def get_external_bin_dir(): 'it get the external bin dir for the running platform and arch' global _EXTERNAL_BIN_DIR if _EXTERNAL_BIN_DIR is not None: return _EXTERNAL_BIN_DIR ext_dir = get_franklin_ext_dir() arch = platform.architecture()[0] system = platform.system().lower() bin_dir = os.path.join(ext_dir, 'bin', system, arch) _EXTERNAL_BIN_DIR = bin_dir return _EXTERNAL_BIN_DIR
def guess_jar_dir(jar_name, java_conf=None): "It returns the jar_name path using locate" conf_variables = { "SortSam.jar": "picard_path", "GenomeAnalysisTK.jar": "gatk_path", "blast2go.jar": "blast2go_path", } java_dir_names = {"SortSam.jar": "picard", "GenomeAnalysisTK.jar": "gatk", "blast2go.jar": "blast2go"} jar_path = None if jar_name in conf_variables: conf_var = conf_variables[jar_name] if java_conf and conf_var in java_conf and java_conf[conf_var]: jar_path = java_conf[conf_var] if not jar_path: if jar_name == "blast2go.jar": jar_path = _guess_java_install_dir(jar_name) else: franklin_path = get_franklin_ext_dir() jar_path = os.path.join(franklin_path, "java", java_dir_names[jar_name]) return jar_path
def guess_jar_dir(jar_name, java_conf=None): 'It returns the jar_name path using locate' conf_variables = {'SortSam.jar': 'picard_path', 'GenomeAnalysisTK.jar': 'gatk_path', 'blast2go.jar': 'blast2go_path'} java_dir_names = {'SortSam.jar': 'picard', 'GenomeAnalysisTK.jar': 'gatk', 'blast2go.jar': 'blast2go'} jar_path = None if jar_name in conf_variables: conf_var = conf_variables[jar_name] if java_conf and conf_var in java_conf and java_conf[conf_var]: jar_path = java_conf[conf_var] if not jar_path: if jar_name == 'blast2go.jar': jar_path = _guess_java_install_dir(jar_name) else: franklin_path = get_franklin_ext_dir() jar_path = os.path.join(franklin_path, 'java', java_dir_names[jar_name]) return jar_path