Genebuild Docker containers

Dockerfiles for Docker containers used in the Genebuild annotation pipeline.

How it works

Dockerfiles are maintained here on GitHub. This repository is mirrored to an internal EBI GitLab instance. When a change is pushed to the default branch on GitHub, it syncs automatically to GitLab, which triggers the CI pipeline defined in .gitlab-ci.yml. GitLab builds the affected container(s) and pushes them to the EBI container registry.

Each container is tagged with both latest and the commit SHA:

registry.gitlab.ebi.ac.uk/<project>/<container-name>:latest
registry.gitlab.ebi.ac.uk/<project>/<container-name>:<commit-sha>

Only containers whose files have changed in a given commit are rebuilt.

Available containers

Containers are listed in the GitLab registry for this project. To browse them, go to the GitLab mirror repository and navigate to Deploy > Container Registry.

Containers currently defined in this repo:

Name	Dockerfile
cpc2	Containers/cpc2/Dockerfile
ensembl-genes	Containers/ensembl-genes/Dockerfile
ensembl-genes-qc-dev	Containers/ensembl-genes-qc-dev/Dockerfile
mirmachine	Containers/mirmachine/Dockerfile
ncrna-mirna	Containers/ncrna-mirna/Dockerfile
star	Containers/star/Dockerfile

Adding a new container

1. Create a directory under Containers/ named after your tool:

   Containers/<name>/Dockerfile
   

2. Add a job block to .gitlab-ci.yml following the pattern used by existing containers:

   build_<name>:
     extends: .build_template
     variables:
       CONTAINER_NAME: <name>
     rules:
       - changes:
           - Containers/<name>/**/*
           - Containers/<name>/*
         when: always

3. Open a PR against the default branch. Once merged, the mirror sync triggers the GitLab pipeline and the container is built and pushed automatically.

Optionally add a README.md inside Containers/<name>/ describing the tool and any usage notes.