cloud_execution.txt

#install the google cloud sdk
#module add  google-cloud-sd *might* be good enough on SCG, but untested
wget https://dl.google.com/dl/cloudsdk/channels/rapid/downloads/google-cloud-sdk-249.0.0-linux-x86_64.tar.gz
#unpack and set up

#now then...
#first time setup
gcloud init #for the time being, must be a non-stanford account (i.e. personal)
gcloud components install kubectl
conda create -n dev python=3.6
source activate dev
pip install --upgrade google-cloud-storage
pip install snakemake

#every time setup
export CLUSTER_NAME=mosscluster
export NODES=12
gcloud container clusters create $CLUSTER_NAME --num-nodes=$NODES --scopes=storage-rw
gcloud container clusters get-credentials $CLUSTER_NAME --region us-central1-a
gcloud auth application-default login #this needs to be the account used for google storage

#work
export REMOTE=GS
export PREFIX=gbsc-gcp-lab-bhatt-user-elimoss/kubernetes
export SNAKEFILE=~/tools/lathe/Snakefile
snakemake -s $SNAKEFILE --kubernetes --use-singularity --default-remote-provider $REMOTE --default-remote-prefix $PREFIX --configfile config.yaml --container-image docker://quay.io/biocontainers/snakemake:5.5.0--0

#this theoretically should do it. unfortunately, I seem to have run into a bug where the prefix is prepended twice, screwing up DAG construction. And that's where I think I'm leaving it.

#teardown
gcloud container clusters delete $CLUSTER_NAME