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Snakemake

The Snakemake workflow management system is a tool to create reproducible and scalable data analyses

Information

Usage

See versions of snakemake which are available:

$ module avail snakemake

Load one version into your environment and run it:

$ module load snakemake/6.15
$ snakemake

Installation

Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/snakemake/6.15
$ sudo chown aorth:aorth /export/apps/snakemake/6.15
$ python3.6 -m venv /export/apps/snakemake/6.15/.venv
$ source /export/apps/snakemake/6.15/.venv/bin/activate
$ pip install --upgrade pip setuptools
$ pip install 'snakemake==6.15.*'
$ sudo chown -R root:root /export/apps/snakemake/6.15