Usage from within the Francis Crick Institute

NOTE: you need to run the main snakemake job on the login node. You need to use tmux or screen sessions for this purpose. In order to reattach a session, you need to be on the same login node where you created the session (login006 or login007).

You can use the environment module system to load singularity (and conda if not already loaded):

1. load anaconda:

ml load Anaconda3/2024.10-1
conda init

2. you can then create and activate a conda environment for snakemake:

conda config --set channel_priority strict
conda create --name pure-faf -c conda-forge -c bioconda snakemake cyvcf2 snakemake-executor-plugin-slurm

# or you can pip install snakemake-executor-plugin-slurm after creating the conda environment:
# pip install snakemake-executor-plugin-slurm

3. create a tmux or screen session and activate the conda environment:

screen -S pure-faf_session
conda activate pure-faf

4. load singularity:

ml load Singularity/3.11.3

Then follow the instructions in the general usage guide to clone the repository, configure and run the workflow. To see an example of snakemake profile configuration for slurm, see turajlic lab usage.