snakemake.deployment package

Submodules

snakemake.deployment.conda module

class snakemake.deployment.conda.Conda(container_img=None, prefix_path=None, check=False)

Bases: object

bin_path()

instances = {}

property is_initialized

lock = <unlocked _thread.lock object>

shellcmd(env_address, cmd)

shellcmd_win(env_address, cmd)

Prepend the windows activate bat script.

class snakemake.deployment.conda.CondaCleanupMode(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: Enum

cache = 'cache'

tarballs = 'tarballs'

class snakemake.deployment.conda.CondaEnvDirSpec(path, rule=None)

Bases: CondaEnvSpec

apply_wildcards(wildcards, rule)

check()

property contains_wildcard

get_conda_env(workflow, envs_dir=None, container_img=None, cleanup=None)

property is_file

class snakemake.deployment.conda.CondaEnvFileSpec(filepath, rule=None)

Bases: CondaEnvSpec

apply_wildcards(wildcards, rule)

check()

property contains_wildcard

get_conda_env(workflow, envs_dir=None, container_img=None, cleanup=None)

property is_file

class snakemake.deployment.conda.CondaEnvNameSpec(name)

Bases: CondaEnvSpec

apply_wildcards(wildcards, _)

check()

property contains_wildcard

get_conda_env(workflow, envs_dir=None, container_img=None, cleanup=None)

class snakemake.deployment.conda.CondaEnvSpec

Bases: ABC

abstract apply_wildcards(wildcards)

abstract check()

abstract property contains_wildcard

abstract get_conda_env(workflow, envs_dir=None, container_img=None, cleanup=None)

property is_file

class snakemake.deployment.conda.CondaEnvSpecType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: Enum

DIR = 'dir'

FILE = 'file'

NAME = 'name'

classmethod from_spec(spec)

class snakemake.deployment.conda.Env(workflow, env_file=None, env_name=None, env_dir=None, envs_dir=None, container_img=None, cleanup=None)

Bases: object

Conda environment from a given specification file.

property address

Path to directory of the conda environment.

First tries full hash, if it does not exist, (8-prefix) is used as default.

property address_argument

property archive_file

Path to archive of the conda environment, which may or may not exist.

check_is_file_based()

property conda

property container_img_url

property content

property content_deploy

property content_hash

property content_pin

create(dryrun=False)

Create the conda environment.

create_archive()

Create self-contained archive of environment.

execute_deployment_script(env_file, deploy_file)

Execute post-deployment script if present

classmethod get_singularity_envvars()

property hash

property is_containerized

property is_externally_managed

Return True if the environment is managed by the user.

property pin_file

property post_deploy_file

snakemake.deployment.conda.get_env_setup_done_flag_file(env_path)

Return type:

Path

snakemake.deployment.containerize module

snakemake.deployment.containerize.containerize(workflow, dag)

snakemake.deployment.env_modules module

class snakemake.deployment.env_modules.EnvModules(*module_names)

Bases: object

property hash: str

shellcmd(cmd)

Return shell command with given modules loaded.

snakemake.deployment.singularity module

class snakemake.deployment.singularity.Image(url, dag, is_containerized)

Bases: object

property hash

property is_local

property path

pull(dryrun=False)

class snakemake.deployment.singularity.Singularity

Bases: object

check()

instance = None

parseversion(raw_version)

property version

snakemake.deployment.singularity.get_snakemake_searchpath_mountpoints()

snakemake.deployment.singularity.shellcmd(img_path, cmd, args='', quiet=False, envvars=None, shell_executable=None, container_workdir=None, is_python_script=False)

Execute shell command inside singularity container given optional args and environment variables to be passed.

Module contents