- recipe snakemake
A popular workflow management system aiming at full in-silico reproducibility.
- Homepage:
- Documentation:
- Developer docs:
- License:
MIT / MIT
- Recipe:
- 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:
9.17.1-1,9.17.1-0,9.16.3-1,9.16.3-0,9.16.2-1,9.16.2-0,9.16.0-0,9.15.0-0,9.14.8-0,9.17.1-1,9.17.1-0,9.16.3-1,9.16.3-0,9.16.2-1,9.16.2-0,9.16.0-0,9.15.0-0,9.14.8-0,9.14.7-0,9.14.6-0,9.14.5-0,9.14.4-0,9.14.3-0,9.14.1-1,9.14.1-0,9.14.0-0,9.13.7-0,9.13.6-0,9.13.5-0,9.13.4-1,9.13.4-0,9.13.3-0,9.13.2-0,9.13.1-0,9.12.0-0,9.11.8-0,9.11.7-0,9.11.6-0,9.11.5-0,9.11.4-0,9.11.3-0,9.11.2-0,9.11.1-0,9.11.0-0,9.10.1-0,9.10.0-0,9.9.0-0,9.8.2-0,9.8.1-0,9.8.0-0,9.7.1-0,9.6.2-0,9.6.1-0,9.6.0-0,9.5.1-0,9.5.0-0,9.4.1-0,9.4.0-0,9.3.5-0,9.3.4-0,9.3.3-0,9.3.2-0,9.3.1-0,9.3.0-0,9.2.0-0,9.1.11-0,9.1.10-0,9.1.9-0,9.1.7-0,9.1.6-0,9.1.5-0,9.1.4-0,9.1.3-0,9.1.2-0,9.1.1-2,9.1.1-0,9.0.1-0,8.30.0-0,8.29.3-0,8.29.2-1,8.29.2-0,8.29.1-0,8.29.0-0,8.28.0-0,8.27.1-0,8.27.0-0,8.26.0-0,8.25.5-0,8.25.4-0,8.25.3-0,8.25.2-0,8.25.1-0,8.25.0-0,8.24.1-0,8.24.0-0,8.23.2-0,8.23.1-0,8.23.0-1,8.23.0-0,8.22.0-0,8.21.0-0,8.20.7-0,8.20.6-0,8.20.5-0,8.20.4-0,8.20.3-0,8.20.1-0,8.18.2-0,8.18.1-0,8.18.0-0,8.17.0-0,8.16.0-0,8.15.2-0,8.15.1-0,8.15.0-0,8.14.0-0,8.13.0-0,8.12.0-0,8.11.6-0,8.11.3-0,8.11.2-0,8.11.1-0,8.11.0-0,8.10.8-1,8.10.8-0,8.10.7-0,8.10.6-0,8.10.5-0,8.10.4-0,8.10.0-0,8.9.0-0,8.8.0-0,8.7.0-0,8.6.0-0,8.5.5-0,8.5.4-0,8.5.3-0,8.5.2-0,8.5.1-0,8.4.12-0,8.4.11-1,8.4.11-0,8.4.9-0,8.4.8-0,8.4.7-0,8.4.6-0,8.4.4-0,8.4.3-0,8.4.2-0,8.4.1-0,8.4.0-0,8.3.2-0,8.2.3-0,8.2.1-0,8.2.0-0,8.1.3-1,8.1.3-0,8.1.2-0,8.1.1-0,8.1.0-0,8.0.1-0,8.0.0-0,7.32.4-1,7.32.4-0,7.32.3-1,7.32.3-0,7.32.2-0,7.32.1-0,7.32.0-0,7.31.1-0,7.31.0-2,7.31.0-1,7.31.0-0,7.30.2-1,7.30.2-0,7.30.1-0,7.30.0-0,7.29.0-0,7.28.3-0,7.28.2-0,7.28.1-0,7.26.0-0,7.25.4-0,7.25.3-0,7.25.2-0,7.25.1-0,7.25.0-1,7.25.0-0,7.24.2-0,7.24.0-1,7.24.0-0,7.22.0-0,7.21.0-0,7.20.0-0,7.19.1-0,7.19.0-0,7.18.2-1,7.18.2-0,7.18.1-0,7.18.0-0,7.17.1-0,7.17.0-0,7.16.0-0,7.15.2-0,7.15.1-0,7.14.2-0,7.14.1-0,7.14.0-0,7.12.1-0,7.12.0-0,7.11.0-0,7.9.0-0,7.8.5-0,7.8.3-0,7.8.2-0,7.8.1-0,7.8.0-0,7.7.0-0,7.6.2-0,7.6.1-1,7.6.1-0,7.6.0-0,7.5.0-0,7.3.8-0,7.3.7-0,7.3.6-0,7.3.5-0,7.3.4-0,7.3.3-0,7.3.2-0,7.3.1-1,7.3.1-0,7.3.0-0,7.2.1-0,7.1.1-0,7.1.0-0,7.0.4-0,7.0.3-0,7.0.2-0,7.0.1-1,7.0.1-0,7.0.0-0,6.15.5-0,6.15.3-0,6.15.2-0,6.15.1-0,6.15.0-0,6.14.0-0,6.13.1-0,6.13.0-0,6.12.3-0,6.12.2-0,6.12.1-0,6.12.0-0,6.11.1-0,6.11.0-0,6.10.0-0,6.9.1-0,6.9.0-0,6.8.2-0,6.8.1-0,6.8.0-0,6.7.0-0,6.6.1-0,6.6.0-0,6.5.3-0,6.5.2-0,6.5.1-0,6.5.0-0,6.4.1-0,6.4.0-0,6.3.0-0,6.2.1-0,6.2.0-0,6.1.2-1,6.1.2-0,6.1.1-0,6.1.0-1,6.1.0-0,6.0.5-1,6.0.5-0,6.0.3-0,6.0.2-0,6.0.1-0,6.0.0-0,5.32.2-0,5.32.1-0,5.32.0-0,5.31.1-1,5.31.1-0,5.31.0-0,5.30.2-0,5.30.1-0,5.29.0-0,5.28.0-0,5.27.4-0,5.26.1-1,5.26.1-0,5.26.0-0,5.25.0-1,5.25.0-0,5.24.2-0,5.24.1-0,5.24.0-1,5.24.0-0,5.23.0-2,5.23.0-1,5.23.0-0,5.22.1-0,5.22.0-0,5.21.0-0,5.20.1-1,5.20.1-0,5.20.0-0,5.19.3-0,5.19.2-0,5.19.1-0,5.19.0-0,5.18.1-0,5.18.0-0,5.17.0-0,5.16.0-0,5.15.0-0,5.14.0-1,5.14.0-0,5.13.0-0,5.12.3-0,5.12.2-0,5.12.1-0,5.11.2-0,5.11.1-0,5.11.0-0,5.10.0-0,5.9.1-0,5.8.2-0,5.8.1-0,5.7.4-0,5.7.1-0,5.7.0-0,5.6.0-0,5.5.4-2,5.5.4-1,5.5.4-0,5.5.3-0,5.5.2-0,5.5.1-0,5.5.0-0,5.4.5-0,5.4.4-0,5.4.3-0,5.4.2-0,5.4.1-0,5.4.0-0,5.3.1-0,5.3.0-2,5.3.0-1,5.2.4-1,5.2.2-1,5.2.1-0,5.2.0-0,5.1.5-0,5.1.4-2,5.1.4-0,5.1.3-0,5.1.2-0,5.1.1-0,5.0.0-0,4.8.1-0,4.8.0-0,4.7.0-0,4.6.0-0,4.5.1-0,4.5.0-0,4.4.0-0,4.3.1-0,4.3.0-0,4.2.0-0,4.1.0-0,4.0.0-1,4.0.0-0,3.13.3-0,3.13.2-0,3.13.0-1,3.12.0-1,3.11.2-1,3.11.2-0,3.11.1-1,3.11.1-0,3.11.0-1,3.10.2-1,3.10.1-1,3.10.1-0,3.10.0-0,3.9.1-0,3.9.0-0,3.8.2-0,3.8.1-0,3.8.0-0,3.7.1-0,3.7.0-0,3.6.1-0,3.6.0-0,3.5.5-1,3.5.4-1,3.5.3-1,3.5.2-1,3.5.1-1,3.4.2-1- Depends:
on eido
on pandas
<3on peppy
on pygments
on slack_sdk
on snakemake-minimal
9.17.1.*
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install snakemake
to add into an existing workspace instead, run:
pixi add snakemake
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install snakemake
Alternatively, to install into a new environment, run:
conda create -n envname snakemake
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/snakemake:<tag>
(see snakemake/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
- package snakemake-minimal¶
- Versions:
9.17.1-1,9.17.1-0,9.16.3-1,9.16.3-0,9.16.2-1,9.16.2-0,9.16.0-0,9.15.0-0,9.14.8-0,9.17.1-1,9.17.1-0,9.16.3-1,9.16.3-0,9.16.2-1,9.16.2-0,9.16.0-0,9.15.0-0,9.14.8-0,9.14.7-0,9.14.6-0,9.14.5-0,9.14.4-0,9.14.3-0,9.14.1-1,9.14.1-0,9.14.0-0,9.13.7-0,9.13.6-0,9.13.5-0,9.13.4-1,9.13.4-0,9.13.3-0,9.13.2-0,9.13.1-0,9.12.0-0,9.11.8-0,9.11.7-0,9.11.6-0,9.11.5-0,9.11.4-0,9.11.3-0,9.11.2-0,9.11.1-0,9.11.0-0,9.10.1-0,9.10.0-0,9.9.0-0,9.8.2-0,9.8.1-0,9.8.0-0,9.7.1-0,9.6.2-0,9.6.1-0,9.6.0-0,9.5.1-0,9.5.0-0,9.4.1-0,9.4.0-0,9.3.5-0,9.3.4-0,9.3.3-0,9.3.2-0,9.3.1-0,9.3.0-0,9.2.0-0,9.1.11-0,9.1.10-0,9.1.9-0,9.1.7-0,9.1.6-0,9.1.5-0,9.1.4-0,9.1.3-0,9.1.2-0,9.1.1-2,9.1.1-0,9.0.1-0,8.30.0-0,8.29.3-0,8.29.2-1,8.29.2-0,8.29.1-0,8.29.0-0,8.28.0-0,8.27.1-0,8.27.0-0,8.26.0-0,8.25.5-0,8.25.4-0,8.25.3-0,8.25.2-0,8.25.1-0,8.25.0-0,8.24.1-0,8.24.0-0,8.23.2-0,8.23.1-0,8.23.0-1,8.23.0-0,8.22.0-0,8.21.0-0,8.20.7-0,8.20.6-0,8.20.5-0,8.20.4-0,8.20.3-0,8.20.1-0,8.18.2-0,8.18.1-0,8.18.0-0,8.17.0-0,8.16.0-0,8.15.2-0,8.15.1-0,8.15.0-0,8.14.0-0,8.13.0-0,8.12.0-0,8.11.6-0,8.11.3-0,8.11.1-0,8.11.0-0,8.10.8-1,8.10.8-0,8.10.7-0,8.10.6-0,8.10.5-0,8.10.4-0,8.10.0-0,8.9.0-0,8.8.0-0,8.7.0-0,8.6.0-0,8.5.5-0,8.5.4-0,8.5.3-0,8.5.2-0,8.5.1-0,8.4.12-0,8.4.11-1,8.4.11-0,8.4.9-0,8.4.8-0,8.4.7-0,8.4.6-0,8.4.4-0,8.4.3-0,8.4.2-0,8.4.1-0,8.4.0-0,8.3.2-0,8.2.3-0,8.2.1-0,8.2.0-0,8.1.3-1,8.1.3-0,8.1.2-0,8.1.1-0,8.1.0-0,8.0.1-0,8.0.0-0,7.32.4-1,7.32.4-0,7.32.3-1,7.32.3-0,7.32.2-0,7.32.1-0,7.32.0-0,7.31.1-0,7.31.0-2,7.31.0-1,7.31.0-0,7.30.2-1,7.30.2-0,7.30.1-0,7.30.0-0,7.29.0-0,7.28.3-0,7.28.2-0,7.28.1-0,7.26.0-0,7.25.4-0,7.25.3-0,7.25.2-0,7.25.1-0,7.25.0-1,7.25.0-0,7.24.2-0,7.24.0-1,7.24.0-0,7.22.0-0,7.21.0-0,7.20.0-0,7.19.1-0,7.19.0-0,7.18.2-1,7.18.2-0,7.18.1-0,7.18.0-0,7.17.1-0,7.17.0-0,7.16.0-0,7.15.2-0,7.15.1-0,7.14.2-0,7.14.1-0,7.14.0-0,7.12.1-0,7.12.0-0,7.11.0-0,7.9.0-0,7.8.5-0,7.8.3-0,7.8.2-0,7.8.1-0,7.8.0-0,7.7.0-0,7.6.2-0,7.6.1-1,7.6.1-0,7.6.0-0,7.5.0-0,7.3.8-0,7.3.7-0,7.3.6-0,7.3.5-0,7.3.4-0,7.3.3-0,7.3.2-0,7.3.1-1,7.3.1-0,7.3.0-0,7.2.1-0,7.1.1-0,7.1.0-0,7.0.4-0,7.0.3-0,7.0.2-0,7.0.1-1,7.0.1-0,7.0.0-0,6.15.5-0,6.15.3-0,6.15.2-0,6.15.1-0,6.15.0-0,6.14.0-0,6.13.1-0,6.13.0-0,6.12.3-0,6.12.2-0,6.12.1-0,6.12.0-0,6.11.1-0,6.11.0-0,6.10.0-0,6.9.1-0,6.9.0-0,6.8.2-0,6.8.1-0,6.8.0-0,6.7.0-0,6.6.1-0,6.6.0-0,6.5.3-0,6.5.2-0,6.5.1-0,6.5.0-0,6.4.1-0,6.4.0-0,6.3.0-0,6.2.1-0,6.2.0-0,6.1.2-1,6.1.2-0,6.1.1-0,6.1.0-1,6.1.0-0,6.0.5-1,6.0.5-0,6.0.3-0,6.0.2-0,6.0.1-0,6.0.0-0,5.32.2-0,5.32.1-0,5.32.0-0,5.31.1-1,5.31.1-0,5.31.0-0,5.30.2-0,5.30.1-0,5.29.0-0,5.28.0-0,5.27.4-0,5.26.1-1,5.26.1-0,5.26.0-0,5.25.0-1,5.25.0-0,5.24.2-0,5.24.1-0,5.24.0-1,5.24.0-0,5.23.0-2,5.22.1-0,5.22.0-0,5.21.0-0,5.20.1-1,5.20.1-0,5.20.0-0,5.19.3-0,5.19.2-0,5.19.1-0,5.19.0-0,5.18.1-0,5.18.0-0,5.17.0-0,5.16.0-0,5.15.0-0,5.14.0-1,5.14.0-0,5.13.0-0,5.12.3-0,5.12.2-0,5.12.1-0,5.11.2-0,5.11.1-0,5.11.0-0,5.10.0-0,5.9.1-0,5.8.2-0,5.8.1-0,5.7.4-0,5.7.1-0,5.7.0-0,5.6.0-0,5.5.4-2,5.5.4-1,5.5.4-0,5.5.3-0,5.5.2-0,5.5.1-0,5.5.0-0,5.4.5-0,5.4.4-1,5.4.3-1,5.4.3-0,5.4.2-1,5.4.2-0,5.4.1-0,5.4.0-0,5.3.1-0,5.3.0-2,5.3.0-1,5.3.0-0,5.2.4-0,5.2.2-1,5.2.2-0,5.2.1-0- Depends:
on appdirs
on conda-inject
>=1.3.1,<2.0on configargparse
on connection_pool
>=0.0.3on docutils
on dpath
>=2.1.6,<3.0.0on gitpython
on humanfriendly
on immutables
on jinja2
>=3.0,<4.0on jsonschema
on nbformat
on packaging
>=24.0on psutil
on pulp
>=2.3.1,<3.4on python
>=3.11,<3.14on pyyaml
on requests
>=2.8.1,<3.0on smart_open
>=4.0,<8.0on snakemake-interface-common
>=1.20.1,<2.0on snakemake-interface-executor-plugins
>=9.3.2,<10.0on snakemake-interface-logger-plugins
>=1.1.0,<3.0.0on snakemake-interface-report-plugins
>=1.2.0,<2.0.0on snakemake-interface-scheduler-plugins
>=2.0.0,<3.0.0on snakemake-interface-storage-plugins
>=4.3.2,<5.0on sqlmodel
>=0.0.37,<0.0.38on tabulate
on tenacity
>=9.1.4,<10.0on throttler
on wrapt
on yte
>=1.5.5,<2.0
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install snakemake-minimal
to add into an existing workspace instead, run:
pixi add snakemake-minimal
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install snakemake-minimal
Alternatively, to install into a new environment, run:
conda create -n envname snakemake-minimal
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/snakemake-minimal:<tag>
(see snakemake-minimal/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/snakemake/README.html)
