Workflow for MAG construction
snakemake -p --verbose --keep-remote -j [number of available cores] --kubernetes -s Snakefile --default-remote-provider GS --default-remote-prefix [GCS Bucket] --use-conda --container-image '[Docker image if different than default]'
Examlpe
snakemake -p --verbose --keep-remote -j 400 --kubernetes -s Snakefilev11 --default-remote-provider GS --default-remote-prefix hn-snakemake --use-conda --container-image 'gcr.io/tagareby/snakemake'
You can start from the sample Dockerfile in this repo which just addes procrps which includes the linux tool free required for megahit -m flag when value less than 1
- Auth docker using gcloud
gcloud auth configure-docker - Build the local DOckerfile
docker build -t [user]/snakemake . - Tag the local image
docker tag [user]/snakemake gcr.io/[project_name]/snakemake - Push the image to the Google Cloud Container Registery
docker push gcr.io/[project]/snakemake