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.

See also Bioconductor Docker Page.

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 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)

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)

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

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

docker images

docker ps

docker ps -a

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

docker pull <name>

docker run -itd <name>

docker stop <name>

docker start <name>

docker rm <name>

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

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>  

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

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

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.

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