Ejemplos de get_gatk_version en Python

Ejemplo n.º 1

Archivo: install.py Proyecto: wangbingqiang/bcbio-nextgen

def get_gatk_jar_version(name, fname):
    if name == "gatk":
        return broad.get_gatk_version(fname)
    elif name == "mutect":
        return broad.get_mutect_version(fname)
    else:
        raise ValueError("Unexpected GATK input: %s" % name)

Ejemplo n.º 2

Archivo: install.py Proyecto: GetBen/bcbio-nextgen

def get_gatk_jar_version(name, fname):
    if name == "gatk":
        return broad.get_gatk_version(fname)
    elif name == "mutect":
        return broad.get_mutect_version(fname)
    else:
        raise ValueError("Unexpected GATK input: %s" % name)

Ejemplo n.º 3

Archivo: gatkfilter.py Proyecto: matthdsm/bcbio-nextgen

def includes_missingalt(data):
    """
    As of GATK 4.1.0.0, variants with missing alts are generated
    (see https://github.com/broadinstitute/gatk/issues/5650)
    """
    MISSINGALT_VERSION = LooseVersion("4.1.0.0")
    version = LooseVersion(broad.get_gatk_version(config=dd.get_config(data)))
    return version >= MISSINGALT_VERSION

Ejemplo n.º 4

Archivo: gatkfilter.py Proyecto: qindan2008/bcbio-nextgen

def includes_missingalt(data):
    """
    As of GATK 4.1.0.0, variants with missing alts are generated
    (see https://github.com/broadinstitute/gatk/issues/5650)
    """
    MISSINGALT_VERSION = LooseVersion("4.1.0.0")
    version = LooseVersion(broad.get_gatk_version(config=dd.get_config(data)))
    return version >= MISSINGALT_VERSION

Ejemplo n.º 5

def includes_missingalt(data):
    """
    As of GATK 4.1.0.0, variants with missing alts are generated
    (see https://github.com/broadinstitute/gatk/issues/5650)
    """
    MISSINGALT_VERSION = LooseVersion("4.1.0.0")
    version = LooseVersion(broad.get_gatk_version(config=dd.get_config(data)))
    try:
        return version >= MISSINGALT_VERSION
    except TypeError:
        logger.error(
            f"LooseVersion failing with {version} as the detected version.")
        sys.exit(1)

Ejemplo n.º 6

Archivo: install.py Proyecto: johnstantongeddes/bcbio-nextgen

def _install_gatk_jar(name, fname, manifest, system_config, toolplus_dir):
    """Install a jar for GATK or associated tools like MuTect.
    """
    if not fname.endswith(".jar"):
        raise ValueError("--toolplus argument for %s expects a jar file: %s" % (name, fname))
    if name == "gatk":
        version = broad.get_gatk_version(fname)
    elif name == "mutect":
        version = broad.get_mutect_version(fname)
    else:
        raise ValueError("Unexpected GATK input: %s" % name)
    store_dir = utils.safe_makedir(os.path.join(toolplus_dir, name, version))
    shutil.copyfile(fname, os.path.join(store_dir, os.path.basename(fname)))
    _update_system_file(system_config, name, {"dir": store_dir})
    _update_manifest(manifest, name, version)

Ejemplo n.º 7

Archivo: install.py Proyecto: snewhouse/bcbio-nextgen

def _install_gatk_jar(name, fname, manifest, system_config, toolplus_dir):
    """Install a jar for GATK or associated tools like MuTect.
    """
    if not fname.endswith(".jar"):
        raise ValueError("--toolplus argument for %s expects a jar file: %s" % (name, fname))
    if name == "gatk":
        version = broad.get_gatk_version(fname)
    elif name == "mutect":
        version = broad.get_mutect_version(fname)
    else:
        raise ValueError("Unexpected GATK input: %s" % name)
    store_dir = utils.safe_makedir(os.path.join(toolplus_dir, name, version))
    shutil.copyfile(fname, os.path.join(store_dir, os.path.basename(fname)))
    _update_system_file(system_config, name, {"dir": store_dir})
    _update_manifest(manifest, name, version)