def install_data_local(config_source,
system_installdir,
data_filedir,
galaxy_home=None,
tool_data_table_conf_file=None,
cores=None,
approaches=None):
"""Local installation of biological data, avoiding fabric usage.
"""
if not cores:
cores = 1
PREP_FNS = {
"s3": _download_s3_index,
"ggd": _install_with_ggd,
"raw": _prep_raw_index
}
if approaches is None: approaches = ["ggd", "s3", "raw"]
ready_approaches = []
Env = collections.namedtuple(
"Env", "system_install, galaxy_home, tool_data_table_conf_file, cores")
env = Env(system_installdir, galaxy_home, tool_data_table_conf_file, cores)
for approach in approaches:
ready_approaches.append((approach, PREP_FNS[approach]))
# Append a potentially custom system install path to PATH so tools are found
os.environ["PATH"] = "%s/bin:%s" % (os.path.join(system_installdir),
os.environ["PATH"])
genomes, genome_indexes, config = _get_genomes(config_source)
genome_indexes = [
x for x in DEFAULT_GENOME_INDEXES if x not in genome_indexes
] + genome_indexes
_make_genome_directories(genomes, data_filedir)
rnaseq.cleanup(genomes, data_filedir)
_prep_genomes(env, genomes, genome_indexes, ready_approaches, data_filedir)
rnaseq.finalize(genomes, data_filedir)
def install_data_s3(config_source):
"""Install data using pre-existing genomes present on Amazon s3.
"""
_check_version()
genomes, genome_indexes, config = _get_genomes(config_source)
genome_indexes += [x for x in DEFAULT_GENOME_INDEXES if x not in genome_indexes]
_make_genome_directories(env, genomes)
rnaseq.cleanup(genomes, env)
_download_genomes(genomes, genome_indexes)
rnaseq.finalize(genomes, env)
_install_additional_data(genomes, genome_indexes, config)
def install_data_s3(config_source):
"""Install data using pre-existing genomes present on Amazon s3.
"""
_check_version()
genomes, genome_indexes, config = _get_genomes(config_source)
genome_indexes += [x for x in DEFAULT_GENOME_INDEXES if x not in genome_indexes]
_make_genome_directories(env, genomes)
rnaseq.cleanup(genomes, env)
_download_genomes(genomes, genome_indexes)
rnaseq.finalize(genomes, env)
_install_additional_data(genomes, genome_indexes, config)
def install_data(config_source, approaches=None):
"""Main entry point for installing useful biological data.
"""
PREP_FNS = {"s3": _download_s3_index,
"ggd": _install_with_ggd,
"raw": _prep_raw_index}
if approaches is None: approaches = ["ggd", "s3", "raw"]
ready_approaches = []
for approach in approaches:
ready_approaches.append((approach, PREP_FNS[approach]))
_check_version()
# Append a potentially custom system install path to PATH so tools are found
with path(os.path.join(env.system_install, 'bin')):
genomes, genome_indexes, config = _get_genomes(config_source)
genome_indexes = [x for x in DEFAULT_GENOME_INDEXES if x not in genome_indexes] + genome_indexes
_make_genome_directories(env, genomes)
rnaseq.cleanup(genomes, env)
_prep_genomes(env, genomes, genome_indexes, ready_approaches)
rnaseq.finalize(genomes, env)
_install_additional_data(genomes, genome_indexes, config)
def install_data(config_source, approaches=None):
"""Main entry point for installing useful biological data.
"""
PREP_FNS = {"s3": _download_s3_index,
"ggd": _install_with_ggd,
"raw": _prep_raw_index}
if approaches is None: approaches = ["ggd", "s3", "raw"]
ready_approaches = []
for approach in approaches:
ready_approaches.append((approach, PREP_FNS[approach]))
_check_version()
# Append a potentially custom system install path to PATH so tools are found
with path(os.path.join(env.system_install, 'bin')):
genomes, genome_indexes, config = _get_genomes(config_source)
genome_indexes = [x for x in DEFAULT_GENOME_INDEXES if x not in genome_indexes] + genome_indexes
_make_genome_directories(env, genomes)
rnaseq.cleanup(genomes, env)
_prep_genomes(env, genomes, genome_indexes, ready_approaches)
rnaseq.finalize(genomes, env)
_install_additional_data(genomes, genome_indexes, config)
def install_data_local(config_source, system_installdir, data_filedir,
galaxy_home=None, tool_data_table_conf_file=None,
cores=None, approaches=None):
"""Local installation of biological data, avoiding fabric usage.
"""
if not cores:
cores = 1
PREP_FNS = {"s3": _download_s3_index,
"ggd": _install_with_ggd,
"raw": _prep_raw_index}
if approaches is None: approaches = ["ggd", "s3", "raw"]
ready_approaches = []
Env = collections.namedtuple("Env", "system_install, galaxy_home, tool_data_table_conf_file, cores")
env = Env(system_installdir, galaxy_home, tool_data_table_conf_file, cores)
for approach in approaches:
ready_approaches.append((approach, PREP_FNS[approach]))
# Append a potentially custom system install path to PATH so tools are found
os.environ["PATH"] = "%s/bin:%s" % (os.path.join(system_installdir), os.environ["PATH"])
genomes, genome_indexes, config = _get_genomes(config_source)
genome_indexes = [x for x in DEFAULT_GENOME_INDEXES if x not in genome_indexes] + genome_indexes
_make_genome_directories(genomes, data_filedir)
rnaseq.cleanup(genomes, data_filedir)
_prep_genomes(env, genomes, genome_indexes, ready_approaches, data_filedir)
rnaseq.finalize(genomes, data_filedir)