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
