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(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)