snakemake toy example

Compliant with JAX HPC Sumner (Cent OS7) using slurm v18.08.8 and minimum Snakemake version 5.14.

Note: Following workflow may need to be tweaked for the newer versions of Snakemake 7.0 or higher. Alternately, you may like a simpler version of snakemake profile from https://github.com/jdblischak/smk-simple-slurm instead of using one given in the profile/sumner/config.yaml directory.

To run

• ssh sumner and clone this repository

mkdir -p ~/pipelines/snakemake
cd ~/pipelines/snakemake

git clone git@github.com:TheJacksonLaboratory/toymake.git
cd toymake

• Edit config.yaml to match your username and valid path for smk_home and workdir.

• Edit Snakefile to match your username (replace amins).

• Setup slurm profile. Read details here first

mkdir -p ~/.config/snakemake/sumner/
rsync -avhP ~/pipelines/snakemake/toymake/profile/sumner/ ~/.config/snakemake/sumner/

• Run workflow

./run_snakemake.sh |& tee -a run.log

• Expected output

end