def _install_data(data_dir, path_flavor, args):
"""Upgrade required genome data files in place.
"""
try:
from bcbio import install as bcb
except:
raise ImportError("It needs bcbio to do the quick installation.")
bio_data = op.join(path_flavor, "../biodata.yaml")
s = {
"flavor": path_flavor,
# "target": "[brew, conda]",
"vm_provider": "novm",
"hostname": "localhost",
"fabricrc_overrides": {
"edition": "minimal",
"use_sudo": "false",
"keep_isolated": "true",
"conda_cmd": bcb._get_conda_bin(),
"distribution": "__auto__",
"dist_name": "__auto__"
}
}
s["actions"] = ["setup_biodata"]
s["fabricrc_overrides"]["data_files"] = data_dir
s["fabricrc_overrides"]["galaxy_home"] = os.path.join(data_dir, "galaxy")
cbl = bcb.get_cloudbiolinux(bcb.REMOTES)
s["genomes"] = _get_biodata(bio_data, args)
sys.path.insert(0, cbl["dir"])
cbl_deploy = __import__("cloudbio.deploy", fromlist=["deploy"])
cbl_deploy.deploy(s)
def _install(path, args):
"""
small helper for installation in case outside bcbio
"""
try:
from bcbio import install as bcb
except:
raise ImportError("It needs bcbio to do the quick installation.")
path_flavor = _get_flavor()
s = {"fabricrc_overrides": {"system_install": path,
"local_install": os.path.join(path, "local_install"),
"use_sudo": "false",
"edition": "minimal"}}
s = {"flavor": path_flavor,
# "target": "[brew, conda]",
"vm_provider": "novm",
"hostname": "localhost",
"fabricrc_overrides": {"edition": "minimal",
"use_sudo": "false",
"keep_isolated": "true",
"conda_cmd": bcb._get_conda_bin(),
"distribution": "__auto__",
"dist_name": "__auto__"}}
s["actions"] = ["install_biolinux"]
s["fabricrc_overrides"]["system_install"] = path
s["fabricrc_overrides"]["local_install"] = os.path.join(path, "local_install")
cbl = bcb.get_cloudbiolinux(bcb.REMOTES)
sys.path.insert(0, cbl["dir"])
cbl_deploy = __import__("cloudbio.deploy", fromlist=["deploy"])
cbl_deploy.deploy(s)
def _install_data(data_dir, path_flavor, args):
"""Upgrade required genome data files in place.
"""
try:
from bcbio import install as bcb
except:
raise ImportError("It needs bcbio to do the quick installation.")
bio_data = op.join(path_flavor, "../biodata.yaml")
s = {"flavor": path_flavor,
# "target": "[brew, conda]",
"vm_provider": "novm",
"hostname": "localhost",
"fabricrc_overrides": {"edition": "minimal",
"use_sudo": "false",
"keep_isolated": "true",
"conda_cmd": bcb._get_conda_bin(),
"distribution": "__auto__",
"dist_name": "__auto__"}}
s["actions"] = ["setup_biodata"]
s["fabricrc_overrides"]["data_files"] = data_dir
s["fabricrc_overrides"]["galaxy_home"] = os.path.join(data_dir, "galaxy")
cbl = bcb.get_cloudbiolinux(bcb.REMOTES)
s["genomes"] = _get_biodata(bio_data, args)
sys.path.insert(0, cbl["dir"])
cbl_deploy = __import__("cloudbio.deploy", fromlist=["deploy"])
cbl_deploy.deploy(s)
def _install(path, args):
"""
small helper for installation in case outside bcbio
"""
try:
from bcbio import install as bcb
except:
raise ImportError("It needs bcbio to do the quick installation.")
path_flavor = _get_flavor()
s = {
"fabricrc_overrides": {
"system_install": path,
"local_install": os.path.join(path, "local_install"),
"use_sudo": "false",
"edition": "minimal"
}
}
s = {
"flavor": path_flavor,
# "target": "[brew, conda]",
"vm_provider": "novm",
"hostname": "localhost",
"fabricrc_overrides": {
"edition": "minimal",
"use_sudo": "false",
"keep_isolated": "true",
"conda_cmd": bcb._get_conda_bin(),
"distribution": "__auto__",
"dist_name": "__auto__"
}
}
s["actions"] = ["install_biolinux"]
s["fabricrc_overrides"]["system_install"] = path
s["fabricrc_overrides"]["local_install"] = os.path.join(
path, "local_install")
cbl = bcb.get_cloudbiolinux(bcb.REMOTES)
sys.path.insert(0, cbl["dir"])
cbl_deploy = __import__("cloudbio.deploy", fromlist=["deploy"])
cbl_deploy.deploy(s)
action='store_true',
default=False,
help="Add ERCC spike-ins.")
parser.add_argument("--mirbase",
help="species in mirbase for smallRNAseq data.")
parser.add_argument("--srna_gtf", help="gtf to use for smallRNAseq data.")
args = parser.parse_args()
if not all([args.mirbase, args.srna_gtf]) and any(
[args.mirbase, args.srna_gtf]):
raise ValueError("--mirbase and --srna_gtf both need a value.")
env.hosts = ["localhost"]
env.cores = args.cores
os.environ["PATH"] += os.pathsep + os.path.dirname(sys.executable)
cbl = get_cloudbiolinux(REMOTES)
sys.path.insert(0, cbl["dir"])
genomemod = __import__("cloudbio.biodata", fromlist=["genomes"])
# monkey patch cloudbiolinux to use this indexing command instead
genomes = getattr(genomemod, 'genomes')
genomes._index_w_command = _index_w_command
fabmod = __import__("cloudbio", fromlist=["fabutils"])
fabutils = getattr(fabmod, 'fabutils')
fabutils.configure_runsudo(env)
system_config = os.path.join(_get_data_dir(), "galaxy",
"bcbio_system.yaml")
with open(system_config) as in_handle:
config = yaml.load(in_handle)
env.picard_home = config_utils.get_program("picard", config, ptype="dir")
help="Name of organism, for example Hsapiens.")
parser.add_argument("-b", "--build", required=True,
help="Build of genome, for example hg19.")
parser.add_argument("-i", "--indexes", choices=SUPPORTED_INDEXES, nargs="*",
default=["seq"], help="Space separated list of indexes to make")
parser.add_argument("--ercc", action='store_true', default=False,
help="Add ERCC spike-ins.")
parser.add_argument("--mirbase", help="species in mirbase for smallRNAseq data.")
parser.add_argument("--srna_gtf", help="gtf to use for smallRNAseq data.")
args = parser.parse_args()
# if not all([args.mirbase, args.srna_gtf]) and any([args.mirbase, args.srna_gtf]):
# raise ValueError("--mirbase and --srna_gtf both need a value.")
os.environ["PATH"] += os.pathsep + os.path.dirname(sys.executable)
cbl = get_cloudbiolinux(REMOTES)
sys.path.insert(0, cbl["dir"])
genomemod = __import__("cloudbio.biodata", fromlist=["genomes"])
# monkey patch cloudbiolinux to use this indexing command instead
genomes = getattr(genomemod, 'genomes')
genomes._index_w_command = _index_w_command
genome_dir = os.path.abspath(os.path.join(_get_data_dir(), "genomes"))
args.fasta = os.path.abspath(args.fasta)
if not file_exists(args.fasta):
print("%s does not exist, exiting." % args.fasta)
sys.exit(1)
args.gtf = os.path.abspath(args.gtf) if args.gtf else None
if args.gtf and not file_exists(args.gtf):
print("%s does not exist, exiting." % args.gtf)
required.add_argument("-f", "--fasta", required=True,
help="FASTA file of the genome.")
required.add_argument("-g", "--gtf", default=None,
help="GTF file of the transcriptome")
required.add_argument("-n", "--name", required=True,
help="Name of organism, for example Hsapiens.")
required.add_argument("-b", "--build", required=True,
help="Build of genome, for example hg19.")
parser.add_argument("--cloudbiolinux", help="Specify a cloudbiolinux git commit hash or tag to install",
default="master")
args = parser.parse_args()
# if not all([args.mirbase, args.srna_gtf]) and any([args.mirbase, args.srna_gtf]):
# raise ValueError("--mirbase and --srna_gtf both need a value.")
os.environ["PATH"] += os.pathsep + os.path.dirname(sys.executable)
cbl = get_cloudbiolinux(args, REMOTES)
sys.path.insert(0, cbl["dir"])
genomemod = __import__("cloudbio.biodata", fromlist=["genomes"])
# monkey patch cloudbiolinux to use this indexing command instead
genomes = getattr(genomemod, 'genomes')
genomes._index_w_command = _index_w_command
genome_dir = os.path.abspath(os.path.join(_get_data_dir(), "genomes"))
args.fasta = os.path.abspath(args.fasta)
if not file_exists(args.fasta):
print("%s does not exist, exiting." % args.fasta)
sys.exit(1)
args.gtf = os.path.abspath(args.gtf) if args.gtf else None
if args.gtf and not file_exists(args.gtf):
print("%s does not exist, exiting." % args.gtf)
