Package Recipe 'snakemake'

recipe snakemake

A popular workflow management system aiming at full in-silico reproducibility.

Homepage:: https://snakemake.github.io
Documentation:: https://snakemake.readthedocs.io/en/stable
Developer docs:: https://github.com/snakemake/snakemake
License:: MIT / MIT
Recipe:: /snakemake/meta.yaml
Links:: doi: 10.1093/bioinformatics/bts480, biotools: snakemake

Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. Snakemake workflows are essentially Python scripts extended by declarative code to define rules. Rules describe how to create output files from input files.

package snakemake¶

versions:

8.25.0-0, 8.24.1-0, 8.24.0-0, 8.23.2-0, 8.23.1-0, 8.23.0-1, 8.23.0-0, 8.22.0-0, 8.21.0-0,
8.25.0-0, 8.24.1-0, 8.24.0-0, 8.23.2-0, 8.23.1-0, 8.23.0-1, 8.23.0-0, 8.22.0-0, 8.21.0-0, 8.20.7-0, 8.20.6-0, 8.20.5-0, 8.20.4-0, 8.20.3-0, 8.20.1-0, 8.18.2-0, 8.18.1-0, 8.18.0-0, 8.17.0-0, 8.16.0-0, 8.15.2-0, 8.15.1-0, 8.15.0-0, 8.14.0-0, 8.13.0-0, 8.12.0-0, 8.11.6-0, 8.11.3-0, 8.11.2-0, 8.11.1-0, 8.11.0-0, 8.10.8-1, 8.10.8-0, 8.10.7-0, 8.10.6-0, 8.10.5-0, 8.10.4-0, 8.10.0-0, 8.9.0-0, 8.8.0-0, 8.7.0-0, 8.6.0-0, 8.5.5-0, 8.5.4-0, 8.5.3-0, 8.5.2-0, 8.5.1-0, 8.4.12-0, 8.4.11-1, 8.4.11-0, 8.4.9-0, 8.4.8-0, 8.4.7-0, 8.4.6-0, 8.4.4-0, 8.4.3-0, 8.4.2-0, 8.4.1-0, 8.4.0-0, 8.3.2-0, 8.2.3-0, 8.2.1-0, 8.2.0-0, 8.1.3-1, 8.1.3-0, 8.1.2-0, 8.1.1-0, 8.1.0-0, 8.0.1-0, 8.0.0-0, 7.32.4-1, 7.32.4-0, 7.32.3-1, 7.32.3-0, 7.32.2-0, 7.32.1-0, 7.32.0-0, 7.31.1-0, 7.31.0-2, 7.31.0-1, 7.31.0-0, 7.30.2-1, 7.30.2-0, 7.30.1-0, 7.30.0-0, 7.29.0-0, 7.28.3-0, 7.28.2-0, 7.28.1-0, 7.26.0-0, 7.25.4-0, 7.25.3-0, 7.25.2-0, 7.25.1-0, 7.25.0-1, 7.25.0-0, 7.24.2-0, 7.24.0-1, 7.24.0-0, 7.22.0-0, 7.21.0-0, 7.20.0-0, 7.19.1-0, 7.19.0-0, 7.18.2-1, 7.18.2-0, 7.18.1-0, 7.18.0-0, 7.17.1-0, 7.17.0-0, 7.16.0-0, 7.15.2-0, 7.15.1-0, 7.14.2-0, 7.14.1-0, 7.14.0-0, 7.12.1-0, 7.12.0-0, 7.11.0-0, 7.9.0-0, 7.8.5-0, 7.8.3-0, 7.8.2-0, 7.8.1-0, 7.8.0-0, 7.7.0-0, 7.6.2-0, 7.6.1-1, 7.6.1-0, 7.6.0-0, 7.5.0-0, 7.3.8-0, 7.3.7-0, 7.3.6-0, 7.3.5-0, 7.3.4-0, 7.3.3-0, 7.3.2-0, 7.3.1-1, 7.3.1-0, 7.3.0-0, 7.2.1-0, 7.1.1-0, 7.1.0-0, 7.0.4-0, 7.0.3-0, 7.0.2-0, 7.0.1-1, 7.0.1-0, 7.0.0-0, 6.15.5-0, 6.15.3-0, 6.15.2-0, 6.15.1-0, 6.15.0-0, 6.14.0-0, 6.13.1-0, 6.13.0-0, 6.12.3-0, 6.12.2-0, 6.12.1-0, 6.12.0-0, 6.11.1-0, 6.11.0-0, 6.10.0-0, 6.9.1-0, 6.9.0-0, 6.8.2-0, 6.8.1-0, 6.8.0-0, 6.7.0-0, 6.6.1-0, 6.6.0-0, 6.5.3-0, 6.5.2-0, 6.5.1-0, 6.5.0-0, 6.4.1-0, 6.4.0-0, 6.3.0-0, 6.2.1-0, 6.2.0-0, 6.1.2-1, 6.1.2-0, 6.1.1-0, 6.1.0-1, 6.1.0-0, 6.0.5-1, 6.0.5-0, 6.0.3-0, 6.0.2-0, 6.0.1-0, 6.0.0-0, 5.32.2-0, 5.32.1-0, 5.32.0-0, 5.31.1-1, 5.31.1-0, 5.31.0-0, 5.30.2-0, 5.30.1-0, 5.29.0-0, 5.28.0-0, 5.27.4-0, 5.26.1-1, 5.26.1-0, 5.26.0-0, 5.25.0-1, 5.25.0-0, 5.24.2-0, 5.24.1-0, 5.24.0-1, 5.24.0-0, 5.23.0-2, 5.23.0-1, 5.23.0-0, 5.22.1-0, 5.22.0-0, 5.21.0-0, 5.20.1-1, 5.20.1-0, 5.20.0-0, 5.19.3-0, 5.19.2-0, 5.19.1-0, 5.19.0-0, 5.18.1-0, 5.18.0-0, 5.17.0-0, 5.16.0-0, 5.15.0-0, 5.14.0-1, 5.14.0-0, 5.13.0-0, 5.12.3-0, 5.12.2-0, 5.12.1-0, 5.11.2-0, 5.11.1-0, 5.11.0-0, 5.10.0-0, 5.9.1-0, 5.8.2-0, 5.8.1-0, 5.7.4-0, 5.7.1-0, 5.7.0-0, 5.6.0-0, 5.5.4-2, 5.5.4-1, 5.5.4-0, 5.5.3-0, 5.5.2-0, 5.5.1-0, 5.5.0-0, 5.4.5-0, 5.4.4-0, 5.4.3-0, 5.4.2-0, 5.4.1-0, 5.4.0-0, 5.3.1-0, 5.3.0-2, 5.3.0-1, 5.2.4-1, 5.2.2-1, 5.2.1-0, 5.2.0-0, 5.1.5-0, 5.1.4-2, 5.1.4-0, 5.1.3-0, 5.1.2-0, 5.1.1-0, 5.0.0-0, 4.8.1-0, 4.8.0-0, 4.7.0-0, 4.6.0-0, 4.5.1-0, 4.5.0-0, 4.4.0-0, 4.3.1-0, 4.3.0-0, 4.2.0-0, 4.1.0-0, 4.0.0-1, 4.0.0-0, 3.13.3-0, 3.13.2-0, 3.13.0-1, 3.12.0-1, 3.11.2-1, 3.11.2-0, 3.11.1-1, 3.11.1-0, 3.11.0-1, 3.10.2-1, 3.10.1-1, 3.10.1-0, 3.10.0-0, 3.9.1-0, 3.9.0-0, 3.8.2-0, 3.8.1-0, 3.8.0-0, 3.7.1-0, 3.7.0-0, 3.6.1-0, 3.6.0-0, 3.5.5-1, 3.5.4-1, 3.5.3-1, 3.5.2-1, 3.5.1-1, 3.4.2-1

depends eido:

depends pandas:

depends peppy:

depends pygments:

depends slack_sdk:

depends snakemake-minimal:

8.25.0.*

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install snakemake

and update with::

   mamba update snakemake

To create a new environment, run:

mamba create --name myenvname snakemake

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/snakemake:<tag>

(see `snakemake/tags`_ for valid values for ``<tag>``)

package snakemake-minimal¶

versions:

8.25.0-0, 8.24.1-0, 8.24.0-0, 8.23.2-0, 8.23.1-0, 8.23.0-1, 8.23.0-0, 8.22.0-0, 8.21.0-0,
8.25.0-0, 8.24.1-0, 8.24.0-0, 8.23.2-0, 8.23.1-0, 8.23.0-1, 8.23.0-0, 8.22.0-0, 8.21.0-0, 8.20.7-0, 8.20.6-0, 8.20.5-0, 8.20.4-0, 8.20.3-0, 8.20.1-0, 8.18.2-0, 8.18.1-0, 8.18.0-0, 8.17.0-0, 8.16.0-0, 8.15.2-0, 8.15.1-0, 8.15.0-0, 8.14.0-0, 8.13.0-0, 8.12.0-0, 8.11.6-0, 8.11.3-0, 8.11.1-0, 8.11.0-0, 8.10.8-1, 8.10.8-0, 8.10.7-0, 8.10.6-0, 8.10.5-0, 8.10.4-0, 8.10.0-0, 8.9.0-0, 8.8.0-0, 8.7.0-0, 8.6.0-0, 8.5.5-0, 8.5.4-0, 8.5.3-0, 8.5.2-0, 8.5.1-0, 8.4.12-0, 8.4.11-1, 8.4.11-0, 8.4.9-0, 8.4.8-0, 8.4.7-0, 8.4.6-0, 8.4.4-0, 8.4.3-0, 8.4.2-0, 8.4.1-0, 8.4.0-0, 8.3.2-0, 8.2.3-0, 8.2.1-0, 8.2.0-0, 8.1.3-1, 8.1.3-0, 8.1.2-0, 8.1.1-0, 8.1.0-0, 8.0.1-0, 8.0.0-0, 7.32.4-1, 7.32.4-0, 7.32.3-1, 7.32.3-0, 7.32.2-0, 7.32.1-0, 7.32.0-0, 7.31.1-0, 7.31.0-2, 7.31.0-1, 7.31.0-0, 7.30.2-1, 7.30.2-0, 7.30.1-0, 7.30.0-0, 7.29.0-0, 7.28.3-0, 7.28.2-0, 7.28.1-0, 7.26.0-0, 7.25.4-0, 7.25.3-0, 7.25.2-0, 7.25.1-0, 7.25.0-1, 7.25.0-0, 7.24.2-0, 7.24.0-1, 7.24.0-0, 7.22.0-0, 7.21.0-0, 7.20.0-0, 7.19.1-0, 7.19.0-0, 7.18.2-1, 7.18.2-0, 7.18.1-0, 7.18.0-0, 7.17.1-0, 7.17.0-0, 7.16.0-0, 7.15.2-0, 7.15.1-0, 7.14.2-0, 7.14.1-0, 7.14.0-0, 7.12.1-0, 7.12.0-0, 7.11.0-0, 7.9.0-0, 7.8.5-0, 7.8.3-0, 7.8.2-0, 7.8.1-0, 7.8.0-0, 7.7.0-0, 7.6.2-0, 7.6.1-1, 7.6.1-0, 7.6.0-0, 7.5.0-0, 7.3.8-0, 7.3.7-0, 7.3.6-0, 7.3.5-0, 7.3.4-0, 7.3.3-0, 7.3.2-0, 7.3.1-1, 7.3.1-0, 7.3.0-0, 7.2.1-0, 7.1.1-0, 7.1.0-0, 7.0.4-0, 7.0.3-0, 7.0.2-0, 7.0.1-1, 7.0.1-0, 7.0.0-0, 6.15.5-0, 6.15.3-0, 6.15.2-0, 6.15.1-0, 6.15.0-0, 6.14.0-0, 6.13.1-0, 6.13.0-0, 6.12.3-0, 6.12.2-0, 6.12.1-0, 6.12.0-0, 6.11.1-0, 6.11.0-0, 6.10.0-0, 6.9.1-0, 6.9.0-0, 6.8.2-0, 6.8.1-0, 6.8.0-0, 6.7.0-0, 6.6.1-0, 6.6.0-0, 6.5.3-0, 6.5.2-0, 6.5.1-0, 6.5.0-0, 6.4.1-0, 6.4.0-0, 6.3.0-0, 6.2.1-0, 6.2.0-0, 6.1.2-1, 6.1.2-0, 6.1.1-0, 6.1.0-1, 6.1.0-0, 6.0.5-1, 6.0.5-0, 6.0.3-0, 6.0.2-0, 6.0.1-0, 6.0.0-0, 5.32.2-0, 5.32.1-0, 5.32.0-0, 5.31.1-1, 5.31.1-0, 5.31.0-0, 5.30.2-0, 5.30.1-0, 5.29.0-0, 5.28.0-0, 5.27.4-0, 5.26.1-1, 5.26.1-0, 5.26.0-0, 5.25.0-1, 5.25.0-0, 5.24.2-0, 5.24.1-0, 5.24.0-1, 5.24.0-0, 5.23.0-2, 5.22.1-0, 5.22.0-0, 5.21.0-0, 5.20.1-1, 5.20.1-0, 5.20.0-0, 5.19.3-0, 5.19.2-0, 5.19.1-0, 5.19.0-0, 5.18.1-0, 5.18.0-0, 5.17.0-0, 5.16.0-0, 5.15.0-0, 5.14.0-1, 5.14.0-0, 5.13.0-0, 5.12.3-0, 5.12.2-0, 5.12.1-0, 5.11.2-0, 5.11.1-0, 5.11.0-0, 5.10.0-0, 5.9.1-0, 5.8.2-0, 5.8.1-0, 5.7.4-0, 5.7.1-0, 5.7.0-0, 5.6.0-0, 5.5.4-2, 5.5.4-1, 5.5.4-0, 5.5.3-0, 5.5.2-0, 5.5.1-0, 5.5.0-0, 5.4.5-0, 5.4.4-1, 5.4.3-1, 5.4.3-0, 5.4.2-1, 5.4.2-0, 5.4.1-0, 5.4.0-0, 5.3.1-0, 5.3.0-2, 5.3.0-1, 5.3.0-0, 5.2.4-0, 5.2.2-1, 5.2.2-0, 5.2.1-0

depends appdirs:

depends conda-inject:

>=1.3.1,<2.0

depends configargparse:

depends connection_pool:

>=0.0.3

depends datrie:

depends docutils:

depends dpath:

>=2.1.6,<3.0.0

depends gitpython:

depends humanfriendly:

depends immutables:

depends jinja2:

>=3.0,<4.0

depends jsonschema:

depends nbformat:

depends packaging:

depends psutil:

depends pulp:

>=2.3.1,<2.10

depends python:

>=3.11,<3.13

depends pyyaml:

depends requests:

>=2.8.1,<3.0

depends reretry:

depends smart_open:

>=4.0,<8.0

depends snakemake-interface-common:

>=1.17.0,<2.0

depends snakemake-interface-executor-plugins:

>=9.3.2,<10.0.0

depends snakemake-interface-report-plugins:

>=1.1.0,<2.0.0

depends snakemake-interface-storage-plugins:

>=3.2.3,<4.0

depends tabulate:

depends throttler:

depends wrapt:

depends yte:

>=1.5.1,<2.0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install snakemake-minimal

and update with::

   mamba update snakemake-minimal

To create a new environment, run:

mamba create --name myenvname snakemake-minimal

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/snakemake-minimal:<tag>

(see `snakemake-minimal/tags`_ for valid values for ``<tag>``)

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/snakemake/README.html)