示例#1
0
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
示例#2
0
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
示例#3
0
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