- Clone or download the repo.
- Modify
config.yaml
to include your data.
To print a description of every rule:
snakemake -l
To print a walkthrough of a google cloud run:
snakemake help
snakemake --configfile config.yaml \
--use-singularity \
--directory /scratch/username/odir \
--keep-remote
snakemake -j 50 --cluster-config amarel.json \
--cluster "sbatch --export=ALL --partition {cluster.partition} --nodes {cluster.n} --time {cluster.time} --ntasks {cluster.tasks} --mem {cluster.mem} --cpus-per-task={cluster.cpus}" \
--keep-remote \
--use-singularity \
--configfile config.yaml \
--directory /scratch/usename/odir
# install prereqs
pip install kubernetes
gcloud components install kubectl
# set up cluster variables
CLUSTER_NAME=snk-cl2
NODES=8
ZONE=us-central1-a
REMOTE=GS
PREFIX=bucket_name
MACHINE_TYPE=n1-standard-2
# initialize cluster
gcloud container clusters create $CLUSTER_NAME \
--num-nodes=$NODES \
--scopes storage-rw \
--machine-type=$MACHINE_TYPE \
--zone $ZONE
# register cluster info
gcloud container clusters get-credentials $CLUSTER_NAME --zone $ZONE
snakemake --kubernetes --use-conda \
--default-remote-provider $REMOTE \
--default-remote-prefix $PREFIX \
--latency-wait 300 \
--jobs 8 \
--verbose
# shut down your cluster
gcloud container clusters delete $CLUSTER_NAME --zone $ZONE