Docker-md5

QC module for any files, based on md5sum.

• Input : a file (either gzipped or not)
• Output : a report file containing regular md5sum (first line) and content (ungzipped) md5sum (second line)
  • format of output report file

  38008d3eb5f7532896c748172427b524
  5a6d311c0d8f6d1dd03c1c129061d3b1
  

The current version of this pipeline pulls the Docker image from a public AWS Elastic Container Registry. If you prefer to pull from Docker Hub (DH), please use the tagged version utilizing DH: v2_DH.

This repo contains the source files for a docker image stored in both 4dndcic/md5:v2 and AWS public.ecr.aws/dcic-4dn/md5:v2.

Cloning the repo

git clone https://github.com/4dn-dcic/docker-md5
cd docker-md5

Resources tools

Major software tools used inside the docker container are downloaded by the script downloads.sh. This script also creates a symlink to a version-independent folder for each software tool. In order to build an updated docker image with a new version of the tools, ideally only downloads.sh should be modified, but not Dockerfile, unless the new tool requires a specific APT tool that need to be downloaded. The downloads.sh file also contains comment lines that specifies the name and version of individual software tools.

Building docker image

You need docker daemon to rebuild the docker image. If you want to push it to a different docker repo, replace 4dndcic/md5:v2 with your desired docker repo name. You need permission to push to 4dndcic/md5:v2.

docker build -t 4dndcic/md5:v2 .
docker push 4dndcic/md5:v2

Usage

Run the following in the container.

run.sh <file> 
# file : input file, either gzipped or not
# output file 'report' is generated.