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(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)