ref_snake

A Snakemake pipeline for genomic reference management

Setup/install

1. Build mamba/conda environment: Note - installing gget with conda has given me issues, I recommend using pip

mamba env create --name ref_snake --file envs/ref_snake.yml

mamba activate ref_snake
pip install gget snakemake
mamba install -c conda-forge pigz

Another note - if you already have these installed on your system, you can update the executable paths in config.yml (EXEC) as they are all called using this info

1. Modify config.yaml to include what species you want to build refs for

SPECIES:
  mus_musculus
  homo_sapiens

1. Run pipeline:

snakemake --use-conda --conda-frontend mamba -j 16

Run pipeline w/ slurm:

snakemake --cluster-config slurm_config.yml --cluster "sbatch -p {cluster.partition} -t {cluster.time} -N {cluster.nodes} --mem {cluster.mem} -o {cluster.output} --cpus-per-task={cluster.threads}" -j 32 --cluster-cancel scancel --use-conda --conda-frontend mamba

Output file tree

See out/README.md for info on the files output for each species

Useful links/resources:

• gget documentation

Misc.

• Download GENCODE references w/ wget

Mus musculus:

wget -e robots=off --recursive --no-parent  https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/latest_release/

optionally, run in the background b/c this takes a while...

nohup wget -e robots=off --recursive --no-parent  https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/latest_release > wget_output.log 2>&1 &

Homo sapiens:

wget -e robots=off --recursive --no-parent  https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/latest_release/

optionally, run in the background b/c this takes a while...

nohup wget -e robots=off --recursive --no-parent  https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/latest_release/ > wget_output.log 2>&1 &