dnousome / dockers

A collection of Dockerfiles to facilitate reproducibility across computing environments.

⚓ Dockers ⚓

This repository contains recipes to Dockers created by CCBR team members to be used :

• in our on-prem pipelines orchestrated using Snakemake and Nextflow. These pipelines run on Biowulf.
• in pipelines running on DNAnexus (and SBG).
• in pipelines running on AWS using AWS Genomics CLI

The docker images were pushed to dockerhub and are available here.

General conventions:

• Each docker image has the following folders:
  • /data2 → Default working directory
  • /opt2 → Tools/software installed inside the docker container go here

NOTE: The suffix 2 ensures that there is no conflict with the hosts' /data and /opt folders.

• Original recipe Dockerfile is copied into the docker image itself in the /opt2 folder.

• Most docker images are built using our own base image nciccbr/ccbr_ubuntu_base_20.04:latest

NOTE: Some of the older docker images may use one of the following base image:

• ubuntu:16.04
• ubuntu:18.04
• bitnami/minideb:jessie : Docker images built using this base image tend to have a smaller digital footprint.

• Docker images should have the following environmental variables:
  • BUILD_DATE
  • BUILD_TAG
  • REPONAME

How the base image nciccbr/ccbr_ubuntu_base_20.04 is built:

• uses ubuntu:20.04 LTS as its base image
• includes /data2 and /opt2 folder
• workdir is always /data2
• contains most commonly used bioinformatics tools like
  • bwa
  • bowtie2
  • samtools
  • bedtools
  • etc.

How to build your own docker image:

• use nciccbr/ccbr_ubuntu_base_20.04:SOMETAG as base image
• add "layers" on top of the base image in order to add tools of interest

Use these lines to kick start your recipe:

FROM nciccbr/ccbr_ubuntu_base_20.04:SOMETAG

# build time variables
ARG BUILD_DATE="000000"
ENV BUILD_DATE=${BUILD_DATE}
ARG BUILD_TAG="000000"
ENV BUILD_TAG=${BUILD_TAG}
ARG REPONAME="000000"
ENV REPONAME=${REPONAME}

# your layers go here!!!

COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}

NOTE: Dockerfile template is available under the resources folder.

• Once your recipe is ready, build and push scripts are from the scripts folder can be used to:
  • automatically build and push built docker images to the nciccbr dockerhub account
  • both scripts take only 1 argument, ie., TAG
  • build expects the folder to contain a file named Dockerfile.TAG which is symlinked to Dockerfile prior to initiating a build
  • build extracts the name of the repo from the current folder name
  • push pushes the built docker over to dockerhub

eg.: Running the following:

> /path/to/scripts/build v2

inside the folder /some/path/ccbr_xyz will

• look for a file Dockerfile.v2 in the folder
• symlink it to Dockerfile
• build a docker with the tag nciccbr/ccbr_xyz:v2

Following this up with:

> /path/to/scripts/path v2

will

• push nciccbr/ccbr_xyz:v2 to Dockerhub
• replace nciccbr/ccbr_xyz:latest with nciccbr/ccbr_xyz:v2 on dockerhub

NOTE: If you are not a member of the nciccbr org on Dockerhub, then you cannot use push script as-in. You may have to modify the dockerhub_account variable appropriately for a successful push.