def _install_additional_data(genomes, config):
download_dbsnp(genomes, BROAD_BUNDLE_VERSION, DBSNP_VERSION)
download_transcripts(genomes, env)
if config.get("install_liftover", False):
lift_over_genomes = [g.ucsc_name() for (_, _, g) in genomes if g.ucsc_name()]
_data_liftover(lift_over_genomes)
if config.get("install_uniref", False):
_data_uniref()
def _install_additional_data(genomes, genome_indexes, config):
download_dbsnp(genomes, BROAD_BUNDLE_VERSION, DBSNP_VERSION)
download_transcripts(genomes, env)
for custom in config.get("custom", []):
_prep_custom_genome(custom, genomes, genome_indexes, env)
if config.get("install_liftover", False):
lift_over_genomes = [g.ucsc_name() for (_, _, g) in genomes if g.ucsc_name()]
_data_liftover(lift_over_genomes)
if config.get("install_uniref", False):
_data_uniref()
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)
download_transcripts(genomes, env)
_download_genomes(genomes, genome_indexes)
_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)
download_transcripts(genomes, env)
_download_genomes(genomes, genome_indexes)
_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,
"raw": _prep_raw_index}
if approaches is None: approaches = ["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]
_make_genome_directories(env, genomes)
download_transcripts(genomes, env)
_prep_genomes(env, genomes, genome_indexes, ready_approaches)
_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,
"raw": _prep_raw_index}
if approaches is None: approaches = ["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]
_make_genome_directories(env, genomes)
download_transcripts(genomes, env)
_prep_genomes(env, genomes, genome_indexes, ready_approaches)
_install_additional_data(genomes, genome_indexes, config)
