Docker containers for Bioconductor
R Dockerfile Ruby Shell
Clone or download
Latest commit 2f4be37 Aug 3, 2018

README.md

Bioconductor Dockers

Overview

This repository contains Dockerfiles for different Docker containers of interest for Bioconductor users. Additional information about available containers, installation and modification can be found on the Bioconductor Docker Page or Docker installation.

Available Docker Containers

See also Bioconductor Docker Page.

Maintained by the Bioconductor Core Team: bioc-issue-bot@bioconductor.org:

Docker Container Docker Hub Latest Version Image Size
release_base2 (GitHub) (DockerHub)
release_core2 (GitHub) (DockerHub)
devel_base2 (GitHub) (DockerHub)
devel_core2 (GitHub) (DockerHub)

Maintained by Steffen Neumann: sneumann@ipb-halle.de

Maintained as part of the “PhenoMeNal, funded by Horizon2020 grant 654241”

Docker Container Docker Hub Latest Version Image Size
release_protmetcore2 (GitHub) (DockerHub)
release_metabolomics2 (GitHub) (DockerHub)
devel_protmetcore2 (GitHub) (DockerHub)
devel_metabolomics2 (GitHub) (DockerHub)

Maintained by Laurent Gatto: lg390@cam.ac.uk

Docker Container Docker Hub Latest Version Image Size
release_mscore2 (GitHub) (DockerHub)
release_protcore2 (GitHub) (DockerHub)
release_proteomics2 (GitHub) (DockerHub)
devel_mscore2 (GitHub) (DockerHub)
devel_protcore2 (GitHub) (DockerHub)
devel_proteomics2 (GitHub) (DockerHub)

General Docker Usage

A well organized guide to popular docker commands can be found here. For convenience, below are some commands to get you started. Note: You may need to add sudo before each command

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>
Get a copy of public docker
docker pull <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 core packages is created from src/core/Dockerfile.in and placed into out/devel_core/Dockerfile.