Bioconductor Dockers - DEPRECATED

Deprecation Notice

These set of images and code have been DEPRECATED in favor of https://github.com/Bioconductor/bioconductor_docker.

We will support the containers till Release 3.11, i.e the current release 3.10 will be the last maintained release.

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	Build status
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	Build status
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	Build status
release_mscore2 (GitHub) (DockerHub)
release_protcore2 (GitHub) (DockerHub)
release_proteomics2 (GitHub) (DockerHub)
devel_mscore2 (GitHub) (DockerHub)
devel_protcore2 (GitHub) (DockerHub)
devel_proteomics2 (GitHub) (DockerHub)

Maintained by RGLab: wjiang2@fredhutch.org

Docker Container	Docker Hub Latest Version	Image Size	Build status
release_cytometry2 (GitHub) (DockerHub)
devel_cytometry2 (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>

Mount a volume

It is possible to mount/map an additional volume or directory. This might be useful for say mounting a local R install directory for use on the docker. The path on the docker image that should be mapped to the additional volume is /usr/local/lib/R/host-site-library. The follow example would mount my locally installed packages to this docker directory. In turn, that path is automatically loaded in the R .libPaths on the docker image and all of my locally installed package would be available for use.

sudo docker run -v /home/lori/R/x86_64-pc-linux-gnu-library/3.5-BioC-3.8:/usr/local/lib/R/host-site-library -it <name>  

User account

If running command line rather than with rstudio, please use the bioc user account

sudo docker run -ti --user bioc <name> R

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.

More Help

Please also see https://bioconductor.org/help/docker/