recipe snakemake

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

Homepage

https://snakemake.readthedocs.io

License

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

(downloads) docker_snakemake

Versions

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 aioeasywebdav

Depends boto3

Depends dropbox

>=7.2.1

Depends filechunkio

>=1.6

Depends ftputil

>=3.2

Depends google-cloud-storage

Depends jinja2

Depends jsonschema

Depends networkx

>=2.0

Depends pandas

Depends psutil

Depends pygraphviz

Depends pysftp

>=0.2.8

Depends python-irodsclient

Depends snakemake-minimal

5.5.2.*

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install snakemake

and update with:

conda update snakemake

or use the docker container:

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

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