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", "--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 _prepare_cwl_tarballs(data_dir):
"""Create CWL ready tarballs for complex directories.
Avoids need for CWL runners to pass and serialize complex directories
of files, which is inconsistent between runners.
"""
for dbref_dir in filter(os.path.isdir, glob.glob(os.path.join(data_dir, "genomes", "*", "*"))):
base_dir, dbref = os.path.split(dbref_dir)
for indexdir in TARBALL_DIRECTORIES:
cur_target = os.path.join(dbref_dir, indexdir)
if os.path.isdir(cur_target):
# Some indices, like rtg, have a single nested directory
subdirs = [x for x in os.listdir(cur_target) if os.path.isdir(os.path.join(cur_target, x))]
if len(subdirs) == 1:
cur_target = os.path.join(cur_target, subdirs[0])
create.directory_tarball(cur_target)
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", "--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 _prepare_cwl_tarballs(data_dir):
"""Create CWL ready tarballs for complex directories.
Avoids need for CWL runners to pass and serialize complex directories
of files, which is inconsistent between runners.
"""
for dbref_dir in filter(
os.path.isdir,
glob.glob(os.path.join(data_dir, "genomes", "*", "*"))):
base_dir, dbref = os.path.split(dbref_dir)
for indexdir in TARBALL_DIRECTORIES:
cur_target = os.path.join(dbref_dir, indexdir)
if os.path.isdir(cur_target):
# Some indices, like rtg, have a single nested directory
subdirs = [
x for x in os.listdir(cur_target)
if os.path.isdir(os.path.join(cur_target, x))
]
if len(subdirs) == 1:
cur_target = os.path.join(cur_target, subdirs[0])
create.directory_tarball(cur_target)
