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.
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.
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) |  |
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| release_core2 (GitHub) (DockerHub) |  |
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| devel_base2 (GitHub) (DockerHub) |  |
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| devel_core2 (GitHub) (DockerHub) |  |
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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) |  |
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| release_metabolomics2 (GitHub) (DockerHub) |  |
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| devel_protmetcore2 (GitHub) (DockerHub) |  |
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| devel_metabolomics2 (GitHub) (DockerHub) |  |
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Maintained by Laurent Gatto: lg390@cam.ac.uk
| Docker Container | Docker Hub Latest Version | Image Size | Build status |
|---|---|---|---|
| release_mscore2 (GitHub) (DockerHub) |  |
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| release_protcore2 (GitHub) (DockerHub) |  |
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| release_proteomics2 (GitHub) (DockerHub) |  |
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| devel_mscore2 (GitHub) (DockerHub) |  |
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| devel_protcore2 (GitHub) (DockerHub) |  |
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| devel_proteomics2 (GitHub) (DockerHub) |  |
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Maintained by RGLab: wjiang2@fredhutch.org
| Docker Container | Docker Hub Latest Version | Image Size | Build status |
|---|---|---|---|
| release_cytometry2 (GitHub) (DockerHub) |  |
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| devel_cytometry2 (GitHub) (DockerHub) |  |
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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/