CeMM Users

Snakemake profile

We created a Snakemake profile and job conductor script for the HPC at CeMM. You can find the repository including documentation and instructions here cemm.slurm.sm.

Migration to Snakemake 8

If you have been a MR.PARETO user for a long time, here are the steps to migrate your setup to Snakemake 8.

1. Install the latest Snakemake version (tested v8.20.1) in a new conda environment.

   conda create -c conda-forge -c bioconda -n snakemake8_20_1 snakemake

2. Install the SLURM executor plugin (tested v0.10.0).

   conda activate snakemake8_20_1
   conda install snakemake-executor-plugin-slurm

3. Pull the latest changes from cemm.slurm.sm.

   cd cemm.slurm.sm
   git pull

4. If you have local clones of MR.PARETO modules pull the latest changes from GitHub, while stashing your modifications.

   cd {module}
   git pull --autostash --rebase

Tip

Make sure conda (and conda-libmamba-solver) are up-to-date.

conda activate base
conda update conda
conda update conda-libmamba-solver