Use a container

Estimated time: 8 minutes

Overview

Questions

• How can I make my workflow more reproducible?
• How do you use a docker image with Snakemake?
• How do I enable containers with snakemake?

Objectives

• Use a container in a rule
• Run snakemake with the –use-singularity argument

Snakemake dependency management

---

• containers
  • exact software versions on later installs
  • support for
    • docker container images
    • singularity container images
• conda environments
  • may result in different software versions on later installs
  • powerful but might not install in every environment

Singularity Container Image URI

---

Pulling a container with docker (won’t work on OSC):

BASH

docker pull alpine:3

OUTPUT

bash: docker: command not found

Pulling a docker container with singularity:

singularity pull docker://alpine:3

Singularity supports multiple container types so you must prefix docker container image URIs with docker://.

Use container when downloading images

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Update the download_image rule to use the docker container image URI quay.io/biocontainers/gnu-wget:1.18--h60da905_7.

rule download_image:
    params: url=get_image_url
    output:'Images/{ark_id}.jpg'
    container: "docker://quay.io/biocontainers/gnu-wget:1.18--h60da905_7"
    shell: "wget -O {output} {params.url}"

NOTE: You must put the container line before the shell line.

Delete an image then run snakemake passing the –use-singularity flag

BASH

rm Images/hd529k3h.jpg
snakemake -c1 --use-singularity Images/hd529k3h.jpg

OUTPUT

Building DAG of jobs...
Pulling singularity image docker://quay.io/biocontainers/gnu-wget:1.18--h60da905_7.
Using shell: /usr/bin/bash
...
Activating singularity image /users/PAS2136/jbradley/SnakemakeWorkflow/.snakemake/singularity/3a63838ec9e2427957182dedc234c8d7.simg
...