wangzhenfei/bioc_docker

Docker containers for Bioconductor

Information about available containers, installation and modification can be found on the Bioconductor Docker Page.

General Docker Usage

List which docker machines are available locally

docker images

List running containers

docker ps

List all containers

docker ps -a

Get container IP address

docker inspect --format '{{ .NetworkSettings.IPAddress }}' <name>

Keep a container running at startup

docker run -itd <name>

Shutdown container

docker stop <name>

Resume container

docker start <name>

Delete container

docker rm <name>

Shell into a running container with either of the following:

docker exec -it <name> /bin/bash
docker attach <name>

Building and modifying the Bioconductor docker images

The BioC Dockerfiles are not directly edited. Instead, for each biocView, there is a common Dockerfile.in, from which two output files for release and devel files are generated by running the rake command. All the creation is controlled by the Rakefile, which will also take care if any of the dependencies (i.e. the *.in files) have changed.

E.g. the Dockerfile for the BioC development branch for Proteomics packages is created from src/proteomics/Dockerfile.in and placed into out/devel_proteomics/Dockerfile.

If you want to build and push an image to dockerhub, copy the auth.yml.template file over to auth.yml, and add your dockerhub credentials. The pushing is done via the docker push command, so for this to succeed you'll have to docker login first. Then all you need is:

rake devel_core