def _upgrade_snpeff_data(galaxy_dir, args, remotes): """Install or upgrade snpEff databases, localized to reference directory. """ for dbkey, ref_file in genome.get_builds(galaxy_dir): resource_file = os.path.join(os.path.dirname(ref_file), "%s-resources.yaml" % dbkey) with open(resource_file) as in_handle: resources = yaml.load(in_handle) snpeff_db, snpeff_base_dir = effects.get_db(ref_file, resources) if snpeff_db: snpeff_db_dir = os.path.join(snpeff_base_dir, snpeff_db) if not os.path.exists(snpeff_db_dir): print("Installing snpEff database %s in %s" % (snpeff_db, snpeff_base_dir)) tooldir = args.tooldir or get_defaults()["tooldir"] config = {"resources": {"snpeff": {"jvm_opts": ["-Xms500m", "-Xmx1g"], "dir": os.path.join(tooldir, "share", "java", "snpeff")}}} raw_version = programs.java_versioner("snpeff", "snpEff", stdout_flag="snpEff version SnpEff")(config) snpeff_version = "".join([x for x in raw_version if x in set(string.digits + ".")]).replace(".", "_") dl_url = remotes["snpeff_dl_url"].format(snpeff_ver=snpeff_version, genome=snpeff_db) dl_file = os.path.basename(dl_url) with utils.chdir(snpeff_base_dir): subprocess.check_call(["wget", "-c", "-O", dl_file, dl_url]) subprocess.check_call(["unzip", dl_file]) os.remove(dl_file) dl_dir = os.path.join(snpeff_base_dir, "data", snpeff_db) os.rename(dl_dir, snpeff_db_dir) os.rmdir(os.path.join(snpeff_base_dir, "data"))
def _upgrade_snpeff_data(galaxy_dir, args, remotes): """Install or upgrade snpEff databases, localized to reference directory. """ for dbkey, ref_file in genome.get_builds(galaxy_dir): resource_file = os.path.join(os.path.dirname(ref_file), "%s-resources.yaml" % dbkey) if os.path.exists(resource_file): with open(resource_file) as in_handle: resources = yaml.load(in_handle) snpeff_db, snpeff_base_dir = effects.get_db({"genome_resources": resources, "reference": {"fasta": {"base": ref_file}}}) if snpeff_db: snpeff_db_dir = os.path.join(snpeff_base_dir, snpeff_db) if not os.path.exists(snpeff_db_dir): print("Installing snpEff database %s in %s" % (snpeff_db, snpeff_base_dir)) tooldir = args.tooldir or get_defaults()["tooldir"] config = {"resources": {"snpeff": {"jvm_opts": ["-Xms500m", "-Xmx1g"], "dir": os.path.join(tooldir, "share", "java", "snpeff")}}} raw_version = programs.java_versioner("snpeff", "snpEff", stdout_flag="snpEff version SnpEff")(config) snpeff_version = "".join([x for x in raw_version if x in set(string.digits + ".")]).replace(".", "_") dl_url = remotes["snpeff_dl_url"].format(snpeff_ver=snpeff_version, genome=snpeff_db) dl_file = os.path.basename(dl_url) with utils.chdir(snpeff_base_dir): subprocess.check_call(["wget", "-c", "-O", dl_file, dl_url]) subprocess.check_call(["unzip", dl_file]) os.remove(dl_file) dl_dir = os.path.join(snpeff_base_dir, "data", snpeff_db) os.rename(dl_dir, snpeff_db_dir) os.rmdir(os.path.join(snpeff_base_dir, "data"))
def _get_snpeff_version(args): tooldir = args.tooldir or get_defaults()["tooldir"] raw_version = programs.get_version_manifest("snpeff") if not raw_version: config = {"resources": {"snpeff": {"jvm_opts": ["-Xms500m", "-Xmx1g"], "dir": os.path.join(tooldir, "share", "java", "snpeff")}}} raw_version = programs.java_versioner("snpeff", "snpEff", stdout_flag="snpEff version SnpEff")(config) snpeff_version = "".join([x for x in raw_version if x in set(string.digits + ".")]).replace(".", "_") assert snpeff_version, "Did not find snpEff version information" return snpeff_version
def _get_snpeff_version(args): tooldir = args.tooldir or get_defaults()["tooldir"] raw_version = programs.get_version_manifest("snpeff") if not raw_version: config = {"resources": {"snpeff": {"jvm_opts": ["-Xms500m", "-Xmx1g"], "dir": os.path.join(tooldir, "share", "java", "snpeff")}}} raw_version = programs.java_versioner("snpeff", "snpEff", stdout_flag="snpEff version SnpEff")(config) snpeff_version = "".join([x for x in raw_version if x in set(string.digits + ".")]).replace(".", "_") assert snpeff_version, "Did not find snpEff version information" return snpeff_version
def snpeff_version(args=None): from bcbio.install import get_defaults tooldir = (args and args.tooldir) or get_defaults()["tooldir"] raw_version = programs.get_version_manifest("snpeff") if not raw_version: config = { "resources": { "snpeff": { "jvm_opts": ["-Xms500m", "-Xmx1g"], "dir": os.path.join(tooldir, "share", "java", "snpeff") } } } raw_version = programs.java_versioner( "snpeff", "snpEff", stdout_flag="snpEff version SnpEff")(config) snpeff_version = "".join( [x for x in str(raw_version) if x in set(string.digits + ".")]) assert snpeff_version, "Did not find snpEff version information" return snpeff_version