Snakemake: Difference between revisions
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Snakemake works with distributions like anaconda to package and install dependencies. I recommend using [[Pyenv]] to keep things organized and separated out. | Snakemake works with distributions like anaconda to package and install dependencies. I recommend using [[Pyenv]] to keep things organized and separated out. | ||
=Installing= | |||
Snakemake is intended to be used in conjunction with Conda, which is a Python tool that enables installing software both inside and outside of the Python ecosystem. | |||
=Links= | =Links= | ||
Revision as of 05:32, 10 February 2018
Snakemake is a pythonic way of writing makefiles.
Snakemake works with distributions like anaconda to package and install dependencies. I recommend using Pyenv to keep things organized and separated out.
Installing
Snakemake is intended to be used in conjunction with Conda, which is a Python tool that enables installing software both inside and outside of the Python ecosystem.
Links
Projects
Snakemake documentation: https://snakemake.readthedocs.io/en/stable/
Snakemake for Bioconda documentation: https://bioconda.github.io/recipes/snakemake/README.html
Snakemake Biocontainer: https://quay.io/repository/biocontainers/snakemake
Examples
A SingleCell RNASeq pre-processing pipeline built on snakemake: https://github.com/Hoohm/dropSeqPipe/blob/master/Snakefile