def _upgrade_snpeff_data(galaxy_dir, args, remotes):
"""Install or upgrade snpEff databases, localized to reference directory.
"""
snpeff_version = effects.snpeff_version(args)
if not snpeff_version:
return
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 os.path.exists(snpeff_db_dir) and _is_old_database(snpeff_db_dir, args):
shutil.rmtree(snpeff_db_dir)
if not os.path.exists(snpeff_db_dir):
print("Installing snpEff database %s in %s" % (snpeff_db, snpeff_base_dir))
dl_url = remotes["snpeff_dl_url"].format(
snpeff_ver=snpeff_version.replace(".", "_"),
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)
shutil.move(dl_dir, snpeff_db_dir)
os.rmdir(os.path.join(snpeff_base_dir, "data"))
def _upgrade_genome_resources(galaxy_dir, base_url):
"""Retrieve latest version of genome resource YAML configuration files.
"""
for dbkey, ref_file in genome.get_builds(galaxy_dir):
# Check for a remote genome resources file
remote_url = base_url % dbkey
requests.packages.urllib3.disable_warnings()
r = requests.get(remote_url, verify=False)
if r.status_code == requests.codes.ok:
local_file = os.path.join(os.path.dirname(ref_file),
os.path.basename(remote_url))
if os.path.exists(local_file):
with open(local_file) as in_handle:
local_config = yaml.load(in_handle)
remote_config = yaml.load(r.text)
needs_update = remote_config["version"] > local_config.get(
"version", 0)
if needs_update:
shutil.move(
local_file,
local_file + ".old%s" % local_config.get("version", 0))
else:
needs_update = True
if needs_update:
print("Updating %s genome resources configuration" % dbkey)
with open(local_file, "w") as out_handle:
out_handle.write(r.text)
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))
dl_url = remotes["snpeff_dl_url"].format(
snpeff_ver=_get_snpeff_version(args), 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)
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.
"""
snpeff_version = effects.snpeff_version(args)
if not snpeff_version:
return
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.safe_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 os.path.exists(snpeff_db_dir) and _is_old_database(snpeff_db_dir, args):
shutil.rmtree(snpeff_db_dir)
if not os.path.exists(snpeff_db_dir):
print("Installing snpEff database %s in %s" % (snpeff_db, snpeff_base_dir))
dl_url = remotes["snpeff_dl_url"].format(
snpeff_ver=snpeff_version.replace(".", "_"),
genome=snpeff_db)
dl_file = os.path.basename(dl_url)
with utils.chdir(snpeff_base_dir):
subprocess.check_call(["wget", "--no-check-certificate", "-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)
shutil.move(dl_dir, snpeff_db_dir)
os.rmdir(os.path.join(snpeff_base_dir, "data"))
if args.cwl:
create.directory_tarball(snpeff_db_dir)
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 upgrade_vcfanno_data(galaxy_dir):
vcfanno_files = _get_vcfanno_files()
vcfanno_remote = REMOTES["vcfanno"]
cmd = "wget --no-check-certificate -O {out_file} {remote_url}"
for dbkey, ref_file in genome.get_builds(galaxy_dir):
build_dir = os.path.abspath(
os.path.join(os.path.dirname(ref_file), os.pardir))
vcfanno_dir = os.path.join(build_dir, "vcfanno")
utils.safe_makedir(vcfanno_dir)
build_files = [x for x in vcfanno_files if x.startswith(dbkey)]
for annofile in build_files:
out_file = os.path.join(vcfanno_dir, annofile)
remote_url = vcfanno_remote + annofile
print cmd.format(**locals())
subprocess.check_call(cmd.format(**locals()), shell=True)
def upgrade_vcfanno_data(galaxy_dir):
vcfanno_files = _get_vcfanno_files()
vcfanno_remote = REMOTES["vcfanno"]
cmd = "wget --no-check-certificate -O {out_file} {remote_url}"
for dbkey, ref_file in genome.get_builds(galaxy_dir):
build_dir = os.path.abspath(os.path.join(os.path.dirname(ref_file),
os.pardir))
vcfanno_dir = os.path.join(build_dir, "vcfanno")
utils.safe_makedir(vcfanno_dir)
build_files = [x for x in vcfanno_files if x.startswith(dbkey)]
for annofile in build_files:
out_file = os.path.join(vcfanno_dir, annofile)
remote_url = vcfanno_remote + annofile
print cmd.format(**locals())
subprocess.check_call(cmd.format(**locals()), shell=True)
def _upgrade_snpeff_data(galaxy_dir, args):
"""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")}}}
snpeff_cmd = effects.get_cmd("download", snpeff_base_dir, config)
subprocess.check_call("%s %s" % (snpeff_cmd, snpeff_db), shell=True)
def _upgrade_genome_resources(galaxy_dir, base_url):
"""Retrieve latest version of genome resource YAML configuration files.
"""
for dbkey, ref_file in genome.get_builds(galaxy_dir):
# Check for a remote genome resources file
remote_url = base_url % dbkey
r = requests.get(remote_url)
if r.status_code == requests.codes.ok:
local_file = os.path.join(os.path.dirname(ref_file), os.path.basename(remote_url))
if os.path.exists(local_file):
with open(local_file) as in_handle:
local_config = yaml.load(in_handle)
remote_config = yaml.load(r.text)
needs_update = remote_config["version"] > local_config.get("version", 0)
if needs_update:
shutil.move(local_file, local_file + ".old%s" % local_config.get("version", 0))
else:
needs_update = True
if needs_update:
print("Updating %s genome resources configuration" % dbkey)
with open(local_file, "w") as out_handle:
out_handle.write(r.text)
def _upgrade_vep_data(galaxy_dir, tooldir):
for dbkey, ref_file in genome.get_builds(galaxy_dir):
effects.prep_vep_cache(dbkey, ref_file, tooldir)
