def _setup_distribution_environment(ignore_distcheck=False):
"""Setup distribution environment
"""
env.logger.info("Distribution %s" % env.distribution)
if env.hosts == ["vagrant"]:
_setup_vagrant_environment()
elif env.hosts == ["localhost"]:
_setup_local_environment()
if env.distribution == "ubuntu":
_setup_ubuntu()
elif env.distribution == "centos":
_setup_centos()
elif env.distribution == "scientificlinux":
_setup_scientificlinux()
elif env.distribution == "debian":
_setup_debian()
else:
raise ValueError("Unexpected distribution %s" % env.distribution)
configure_runsudo(env)
if not ignore_distcheck:
_validate_target_distribution(env.distribution, env.get('dist_name', None))
_cloudman_compatibility(env)
_setup_nixpkgs()
_setup_fullpaths(env)
# allow us to check for packages only available on 64bit machines
machine = env.safe_run_output("uname -m")
env.is_64bit = machine.find("_64") > 0
def _setup_distribution_environment(ignore_distcheck=False):
"""Setup distribution environment
"""
env.logger.info("Distribution %s" % env.distribution)
if env.hosts == ["vagrant"]:
_setup_vagrant_environment()
elif env.hosts == ["localhost"]:
_setup_local_environment()
if env.distribution == "ubuntu":
_setup_ubuntu()
elif env.distribution == "centos":
_setup_centos()
elif env.distribution == "scientificlinux":
_setup_scientificlinux()
elif env.distribution == "debian":
_setup_debian()
else:
raise ValueError("Unexpected distribution %s" % env.distribution)
configure_runsudo(env)
if not ignore_distcheck:
_validate_target_distribution(env.distribution,
env.get('dist_name', None))
_cloudman_compatibility(env)
_setup_nixpkgs()
_setup_fullpaths(env)
# allow us to check for packages only available on 64bit machines
machine = env.safe_run_output("uname -m")
env.is_64bit = machine.find("_64") > 0
def _setup_distribution_environment(ignore_distcheck=False):
"""Setup distribution environment.
In low-level terms, this method attempts to populate various values in the fabric
env data structure for use other places in CloudBioLinux.
"""
if "distribution" not in env:
env.distribution = "__auto__"
if "dist_name" not in env:
env.dist_name = "__auto__"
env.logger.info("Distribution %s" % env.distribution)
if env.hosts == ["vagrant"]:
_setup_vagrant_environment()
elif env.hosts == ["localhost"]:
_setup_local_environment()
configure_runsudo(env)
if env.distribution == "__auto__":
env.distribution = _determine_distribution(env)
if env.distribution == "ubuntu":
## TODO: Determine if dist_name check works with debian.
if env.dist_name == "__auto__":
env.dist_name = _ubuntu_dist_name(env)
_setup_ubuntu()
elif env.distribution == "centos":
_setup_centos()
elif env.distribution == "scientificlinux":
_setup_scientificlinux()
elif env.distribution == "debian":
if env.dist_name == "__auto__":
env.dist_name = _debian_dist_name(env)
_setup_debian()
elif env.distribution == "arch":
pass # No package support for Arch yet
elif env.distribution == "suse":
pass # No package support for SUSE yet
elif env.distribution == "macosx":
_setup_macosx(env)
ignore_distcheck = True
else:
raise ValueError("Unexpected distribution %s" % env.distribution)
if not ignore_distcheck:
_validate_target_distribution(env.distribution,
env.get('dist_name', None))
_cloudman_compatibility(env)
_setup_nixpkgs()
_setup_fullpaths(env)
# allow us to check for packages only available on 64bit machines
machine = env.safe_run_output("uname -m")
env.is_64bit = machine.find("_64") > 0
def _setup_distribution_environment(ignore_distcheck=False):
"""Setup distribution environment.
In low-level terms, this method attempts to populate various values in the fabric
env data structure for use other places in CloudBioLinux.
"""
if "distribution" not in env:
env.distribution = "__auto__"
if "dist_name" not in env:
env.dist_name = "__auto__"
env.logger.info("Distribution %s" % env.distribution)
if env.hosts == ["vagrant"]:
_setup_vagrant_environment()
elif env.hosts == ["localhost"]:
_setup_local_environment()
configure_runsudo(env)
if env.distribution == "__auto__":
env.distribution = _determine_distribution(env)
if env.distribution == "ubuntu":
## TODO: Determine if dist_name check works with debian.
if env.dist_name == "__auto__":
env.dist_name = _ubuntu_dist_name(env)
_setup_ubuntu()
elif env.distribution == "centos":
_setup_centos()
elif env.distribution == "scientificlinux":
_setup_scientificlinux()
elif env.distribution == "debian":
if env.dist_name == "__auto__":
env.dist_name = _debian_dist_name(env)
_setup_debian()
elif env.distribution == "arch":
pass # No package support for Arch yet
elif env.distribution == "suse":
pass # No package support for SUSE yet
elif env.distribution == "macosx":
_setup_macosx(env)
ignore_distcheck = True
else:
raise ValueError("Unexpected distribution %s" % env.distribution)
if not ignore_distcheck:
_validate_target_distribution(env.distribution, env.get('dist_name', None))
_cloudman_compatibility(env)
_setup_nixpkgs()
_setup_fullpaths(env)
# allow us to check for packages only available on 64bit machines
machine = env.safe_run_output("uname -m")
env.is_64bit = machine.find("_64") > 0
parser.add_argument("-n", "--name", required=True,
help="Name of genome.")
parser.add_argument("-b", "--build", required=True,
help="Build of genome.")
parser.add_argument("-d", "--genome-dir", required=True,
help="Path to bcbio-nextgen genomes directory.")
parser.add_argument("-i", "--indexes", choices=genomes.INDEX_FNS.keys(),
nargs="*", required=True,
help="List of indexes to make")
parser.add_argument("-p", "--picard-dir", default=None,
help="Path to Picard installation")
parser.add_argument("--prepare-tx", default=None,
help="Path to prepare_tx_gff.py (in utils/cloudbiolinux)")
args = parser.parse_args()
fabutils.configure_runsudo(env)
args.genome_dir = os.path.abspath(args.genome_dir)
args.fasta = os.path.abspath(args.fasta)
args.gtf = os.path.abspath(args.gtf) if args.gtf else None
env.system_install = args.genome_dir
print "Creating directories using %s as the base." % (args.genome_dir)
build_dir = setup_base_directories(args.genome_dir, args.name,
args.build, args.gtf)
os.chdir(build_dir)
print "Genomes will be installed into %s." % (build_dir)
fasta_file = install_fasta_file(build_dir, args.fasta, args.build)
print "Installed genome as %s." % (fasta_file)
if args.gtf:
gtf_file = install_gtf_file(build_dir, args.gtf, args.build)
choices=genomes.INDEX_FNS.keys(),
nargs="*",
required=True,
help="List of indexes to make")
parser.add_argument("-p",
"--picard-dir",
default=None,
help="Path to Picard installation")
parser.add_argument(
"--prepare-tx",
default=None,
help="Path to prepare_tx_gff.py (in utils/cloudbiolinux)")
args = parser.parse_args()
env.hosts = ["localhost"]
fabutils.configure_runsudo(env)
args.genome_dir = os.path.abspath(args.genome_dir)
args.fasta = os.path.abspath(args.fasta)
args.gtf = os.path.abspath(args.gtf) if args.gtf else None
env.system_install = args.genome_dir
print "Creating directories using %s as the base." % (args.genome_dir)
build_dir = setup_base_directories(args.genome_dir, args.name, args.build,
args.gtf)
os.chdir(build_dir)
print "Genomes will be installed into %s." % (build_dir)
fasta_file = install_fasta_file(build_dir, args.fasta, args.build)
print "Installed genome as %s." % (fasta_file)
if args.gtf:
gtf_file = install_gtf_file(build_dir, args.gtf, args.build)