def install_data_ggd(recipe, organism): """Install data using Get Genomics Data (GGD) recipes. """ setup_environment() from cloudbio.biodata import ggd, genomes genome_dir = os.path.join(genomes._make_genome_dir(), organism) ggd.install_recipe(genome_dir, recipe)
def install_data_ggd(recipe, organism): """Install data using Get Genomics Data (GGD) recipes. """ setup_environment() from cloudbio.biodata import ggd, genomes genome_dir = os.path.join(genomes._make_genome_dir(), organism) recipe_file = os.path.join(os.path.dirname(__file__), "ggd-recipes", organism, "%s.yaml" % recipe) ggd.install_recipe(genome_dir, recipe_file)
def _install_with_ggd(env, manager, gid, recipe): recipe_dir = os.path.normpath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "ggd-recipes")) recipe_file = os.path.join(recipe_dir, gid, "%s.yaml" % recipe) if os.path.exists(recipe_file): ggd.install_recipe(os.getcwd(), env.system_install, recipe_file, gid) else: raise NotImplementedError("GGD recipe not available for %s %s" % (gid, recipe))
def install_data_ggd(recipe, organism): """Install data using Get Genomics Data (GGD) recipes. """ setup_environment() from cloudbio.biodata import ggd, genomes genome_dir = os.path.join(genomes._make_genome_dir(), organism) recipe_file = os.path.join(os.path.dirname(__file__), "ggd-recipes", organism, "%s.yaml" % recipe) ggd.install_recipe(genome_dir, env, recipe_file, organism)
def _install_with_ggd(env, manager, gid, recipe): assert env.hosts == ["localhost"], "GGD recipes only work for local runs" recipe_dir = os.path.normpath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "ggd-recipes")) recipe_file = os.path.join(recipe_dir, gid, "%s.yaml" % recipe) if os.path.exists(recipe_file): ggd.install_recipe(env.cwd, recipe_file, gid) else: raise NotImplementedError("GGD recipe not available for %s %s" % (gid, recipe))
def _install_with_ggd(env, manager, gid, idx): assert env.hosts == ["localhost"], "GGD recipes only work for local runs" recipe_dir = os.path.normpath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "ggd-recipes")) recipes = [idx] if idx in ["seq"]: if manager.config.get("dbsnp"): recipes.append("dbsnp-%s" % manager.config["dbsnp"]) if manager.config.get("rnaseq"): recipes.append("rnaseq") done = False for recipe in recipes: recipe_file = os.path.join(recipe_dir, gid, "%s.yaml" % recipe) if os.path.exists(recipe_file): ggd.install_recipe(env.cwd, recipe_file) done = True if not done: raise NotImplementedError("GGD recipe not available for %s %s" % (gid, idx))