https://github.com/bioconductor/bioc_docker
[DEPRECATED] Docker containers for Bioconductor
https://github.com/bioconductor/bioc_docker
bioconductor-dockers
Last synced: 11 months ago
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[DEPRECATED] Docker containers for Bioconductor
- Host: GitHub
- URL: https://github.com/bioconductor/bioc_docker
- Owner: Bioconductor
- License: artistic-2.0
- Created: 2014-12-22T22:44:51.000Z (over 11 years ago)
- Default Branch: devel
- Last Pushed: 2023-03-15T20:25:37.000Z (about 3 years ago)
- Last Synced: 2025-04-28T05:35:05.184Z (about 1 year ago)
- Topics: bioconductor-dockers
- Language: R
- Homepage: https://github.com/bioconductor/bioconductor_docker
- Size: 4 MB
- Stars: 49
- Watchers: 19
- Forks: 26
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# 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](http://bioconductor.org/help/docker/) or [Docker
installation](https://docs.docker.com/installation/).
## Available Docker Containers ##
See also [Bioconductor Docker Page](http://bioconductor.org/help/docker/).
#### Maintained by the Bioconductor Core Team: bioc-issue-bot@bioconductor.org:
| Docker Container | Docker Hub Latest Version | Image Size | Build status
| :------------------------- | :----------------- | :---------- | :----------
| release_base2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_base)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_base2/)) | [](https://hub.docker.com/r/bioconductor/release_base2/) | [](https://hub.docker.com/r/bioconductor/release_base2/)| [](https://hub.docker.com/r/bioconductor/release_base2/builds/)
| release_core2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_core)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_core2/)) | [](https://hub.docker.com/r/bioconductor/release_core2/) | [](https://hub.docker.com/r/bioconductor/release_core2/) | [](https://hub.docker.com/r/bioconductor/release_core2/builds/)
| devel_base2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_base)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_base2/)) | [](https://hub.docker.com/r/bioconductor/devel_base2/) | [](https://hub.docker.com/r/bioconductor/devel_base2/) | [](https://hub.docker.com/r/bioconductor/devel_base2/builds/)
| devel_core2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_core)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_core2/)) | [](https://hub.docker.com/r/bioconductor/devel_core2/) | [](https://hub.docker.com/r/bioconductor/devel_core2/) | [](https://hub.docker.com/r/bioconductor/devel_core2/builds/)
#### 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](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_protmetcore)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_protmetcore2/)) | [](https://hub.docker.com/r/bioconductor/release_protmetcore2/) | [](https://hub.docker.com/r/bioconductor/release_protmetcore2/) | [](https://hub.docker.com/r/bioconductor/release_protmetcore2/builds/)
| release_metabolomics2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_metabolomics)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_metabolomics2/)) | [](https://hub.docker.com/r/bioconductor/release_metabolomics2/) | [](https://hub.docker.com/r/bioconductor/release_metabolomics2/) | [](https://hub.docker.com/r/bioconductor/release_metabolomics2/builds/)
| devel_protmetcore2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_protmetcore)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_protmetcore2/)) | [](https://hub.docker.com/r/bioconductor/devel_protmetcore2/) | [](https://hub.docker.com/r/bioconductor/devel_protmetcore2/) | [](https://hub.docker.com/r/bioconductor/devel_protmetcore2/builds/)
| devel_metabolomics2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_metabolomics)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_metabolomics2/)) | [](https://hub.docker.com/r/bioconductor/devel_metabolomics2/) | [](https://hub.docker.com/r/bioconductor/devel_metabolomics2/) | [](https://hub.docker.com/r/bioconductor/devel_metabolomics2/builds/)
#### Maintained by Laurent Gatto: lg390@cam.ac.uk
| Docker Container | Docker Hub Latest Version | Image Size | Build status
| :------------------------- | :----------------- | :---------- | :----------
| release_mscore2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_mscore)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_mscore2/)) | [](https://hub.docker.com/r/bioconductor/release_mscore2/) | [](https://hub.docker.com/r/bioconductor/release_mscore2/) | [](https://hub.docker.com/r/bioconductor/release_mscore2/builds/)
| release_protcore2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_protcore)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_protcore2/)) | [](https://hub.docker.com/r/bioconductor/release_protcore2/) | [](https://hub.docker.com/r/bioconductor/release_protcore2/) | [](https://hub.docker.com/r/bioconductor/release_protcore2/builds/)
| release_proteomics2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_proteomics)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_proteomics2/)) | [](https://hub.docker.com/r/bioconductor/release_proteomics2/) | [](https://hub.docker.com/r/bioconductor/release_proteomics2/) | [](https://hub.docker.com/r/bioconductor/release_proteomics2/builds/)
| devel_mscore2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_mscore)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_mscore2/)) | [](https://hub.docker.com/r/bioconductor/devel_mscore2/) | [](https://hub.docker.com/r/bioconductor/devel_mscore2/) | [](https://hub.docker.com/r/bioconductor/devel_mscore2/builds/)
| devel_protcore2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_protcore)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_protcore2/)) | [](https://hub.docker.com/r/bioconductor/devel_protcore2/) | [](https://hub.docker.com/r/bioconductor/devel_protcore2/) | [](https://hub.docker.com/r/bioconductor/devel_protcore2/builds/)
| devel_proteomics2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_proteomics)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_proteomics2/)) | [](https://hub.docker.com/r/bioconductor/devel_proteomics2/) | [](https://hub.docker.com/r/bioconductor/devel_proteomics2/) | [](https://hub.docker.com/r/bioconductor/devel_proteomics2/builds/)
#### Maintained by RGLab: wjiang2@fredhutch.org
| Docker Container | Docker Hub Latest Version | Image Size | Build status
| :------------------------- | :----------------- | :---------- | :----------
| release_cytometry2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_cytometry)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_cytometry2/)) | [](https://hub.docker.com/r/bioconductor/release_cytometry2/) | [](https://hub.docker.com/r/bioconductor/release_cytometry2/) | [](https://hub.docker.com/r/bioconductor/release_cytometry2/builds/)
| devel_cytometry2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_cytometry)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_cytometry2/)) | [](https://hub.docker.com/r/bioconductor/devel_cytometry2/) | [](https://hub.docker.com/r/bioconductor/devel_cytometry2/) | [](https://hub.docker.com/r/bioconductor/devel_cytometry2/builds/)
### General Docker Usage
A well organized guide to popular docker commands can be found
[here](https://github.com/wsargent/docker-cheat-sheet). 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 }}'
##### Get a copy of public docker
docker pull
##### Keep a container running at startup
docker run -itd
##### Shutdown container
docker stop
##### Resume container
docker start
##### Delete container
docker rm
##### Shell into a running container with either of the following:
docker exec -it /bin/bash
docker attach
##### 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
##### User account
If running command line rather than with rstudio, please use the bioc user
account
sudo docker run -ti --user bioc 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/