docker-snakemake

A set of best practice Dockerfiles to build containers for running and developing Snakemake workflows.

Images

snakemake-minimal

• Includes the bare minimum requirements for running Snakemake in a local environment.

snakemake-full

• Includes all dependencies for running Snakemake in any kind of environment.

snakemake-base

• This is the base image that the above images are based off of. You don't want to use this image directly unless you plan to customize your own image.
• What it does:
  • Installs gosu
  • Adds a docker-entrypoint.sh file
  • Adds a snakemake user and group with uid=gid=1000 to run Snakemake as a non-root user
  • Sets the snakemake user to automatically activate the snakemake conda environment

Building & Running

snakemake-minimal

docker build --tag snakemake-base ./snakemake-base
docker build --tag snakemake-minimal ./snakemake-minimal
docker run --rm -it snakemake-minimal

snakemake-full

docker build --tag snakemake-base ./snakemake-base
docker build --tag snakemake-full ./snakemake-full
docker run --rm -it snakemake-full