Python install_recipe Exemples

Exemple #1

Fichier : data_fabfile.py Projet : MauricioCarneiro/cloudbiolinux

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)

Exemple #2

Fichier : data_fabfile.py Projet : Fredus14/cloudbiolinux

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)

Exemple #3

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))

Exemple #4

Fichier : data_fabfile.py Projet : wangdi2014/cloudbiolinux

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)

Exemple #5

Fichier : genomes.py Projet : chapmanb/cloudbiolinux

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))

Exemple #6

Fichier : genomes.py Projet : pombredanne/cloudbiolinux

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))

Exemple #7

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))

Exemple #8

Fichier : genomes.py Projet : scatreux/cloudbiolinux

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))