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https://github.com/bioconductor/bioconductor_full
DEPRECATED - Docker Images which include a complete installation of all software needed to build all Bioconductor packages
https://github.com/bioconductor/bioconductor_full
bioconductor containers docker
Last synced: about 1 month ago
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DEPRECATED - Docker Images which include a complete installation of all software needed to build all Bioconductor packages
- Host: GitHub
- URL: https://github.com/bioconductor/bioconductor_full
- Owner: Bioconductor
- License: gpl-2.0
- Created: 2019-02-22T19:31:48.000Z (almost 6 years ago)
- Default Branch: devel
- Last Pushed: 2023-03-15T21:04:28.000Z (almost 2 years ago)
- Last Synced: 2024-05-09T07:47:29.670Z (8 months ago)
- Topics: bioconductor, containers, docker
- Language: Dockerfile
- Homepage: http://bioconductor.org/help/docker/
- Size: 67.4 KB
- Stars: 26
- Watchers: 10
- Forks: 4
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Bioconductor Devel Docker image - DEPRECATED
**Deprecation Notice** : The `bioconductor/bioconductor_full` images have been deprecated in favor of the new `bioconductor/bioconductor_docker` images located at https://github.com/bioconductor/bioconductor_docker . These new images will have the same functionality as `bioconductor_full`, and users should find it easy to switch between the new set of containers. Please refer to the [README.md](https://github.com/Bioconductor/bioconductor_docker/blob/master/README.md) of the new images for more information.
Bioconductor Docker image with full set of system dependencies so that
all Bioconductor packages can be installed.
The Docker images have R and Bioconductor with different versions
under each "branch" in git.
**NOTE**: Docker image for bioconductor_full:devel is in the `master`
branch, and all the release branches will be under the branch
`RELEASE_X_Y`.
Important Links:
[Docker hub link for bioconductor_full](https://hub.docker.com/r/bioconductor/bioconductor_full)
[Github development link for bioconductor_full](https://github.com/Bioconductor/bioconductor_full)
## Advantages of the `bioconductor_full` docker image
1. The bioconductor_full docker images can be used instead of
installing complex dependencies needed for Bioconductor
packages. The image comes with most of the dependencies installed.
1. Quick start up to start your analysis with all the Bioconductor
packages if needed.
1. The image will be regularly updated to reflect the build system on
Bioconductor. This is a very useful resource for maintainers who
are actively developing their package to see if it works in tandem
with the bioconductor ecosystem. It provides a local testing outlet
for maintainers and developers.
## Installation and quick start
This document assumes you have [docker][] installed. Please check
[installation][] if you have more questions regarding this.
[docker]: https://www.docker.com/
[installation]: https://www.docker.com/products/docker-desktop
### Quick start
* Start docker on your machine.
* On the command line, "pull" the bioconductor_full docker image with
the correct tag. These images are hosted on docker hub under the
[Bioconductor organization][] page.
docker pull bioconductor/bioconductor_full:devel
or
docker pull bioconductor/bioconductor_full:RELEASE_X_Y
* Once the image is available on your local machine, you can check to
see if they are available.
docker images
* To start using these images with RStudio, this will start the image
under the 'rstudio' user
docker run \
-e PASSWORD=your_password \
-p 8787:8787 \
-v ~/host-site-library:/usr/local/lib/R/host-site-library \
bioconductor/bioconductor_full:devel
* To start the image interactively using the `bioc` user
docker run \
-it \
--user bioc \
-v ~/host-site-library:/usr/local/lib/R/host-site-library \
bioconductor/bioconductor_full:devel \
R
NOTE: The path `/usr/local/lib/R/host-site-library` is mapped to
`.libPaths()` in R. So, when R is started, all the libraries in
the host directory, `host-site-library` are available to R. It is
stored on your machine mounted from the volume you fill in place
of `host-site-library`.
These libraries will only work if they are pre-compiled with the
same version of R that is in the docker image. To explain further,
you would need the packages built with Bioconductor version '3.9'
to work with R-3.6. Similarly, you'd need Bioconductor version
'3.9' to work with R-3.6.z.
* To start the docker image in deamon mode, i.e, have the container
running in the background use the `-d` option.
sudo docker run -it \
-d \
-v host-site-library:/usr/local/lib/R/host-site-library \
--entrypoint /bin/bash \
bioconductor/bioconductor_full:devel
This will start the container in the background and keep it
running. You may check the running processes using `docker ps`,
and copy the container id.
docker ps
To attach to a container which is running in the background
docker exec -it bash
NOTE: You can replace `bash` with R to start R directly in the
container.
docker exec -it R
* To run multiple RStudio instances, use a different external port
mapping (the first port in `-p XXXX:YYYY`) for each instance.
Use standard shell commands (e.g., adding a `&` at the end of the
first docker command) to place docker processes in the
background. The 'devel' instance will be available at
http://localhost:8787, and the release image at
http://localhost:8788
docker run \
-e PASSWORD=your_password \
-p 8787:8787 \
bioconductor/bioconductor_full:devel
docker run \
-e PASSWORD=your_password \
-p 8788:8787 \
bioconductor/bioconductor_full:RELEASE_3_10
## Issues in the devel image
### Packages which will never install
1. xps
1. Rmpi
1. ccfindR
For more information on the issues for this image, please check
`issues.md`
## Singularity
Bioconductor provides singularity hub images. The files Singularity, Singularity.RELEASE_3_8, Singularity.RELEASE_3_9 allow the images to build on Singularity hub.
Find the singularity hub images, and download them by https://www.singularity-hub.org/collections/3154/usage
singularity pull shub://Bioconductor/bioconductor_full
## Frequently Asked Questions (FAQ)
### How do I use LaTeX inside the container?
Install the `tinytex` package (https://yihui.name/tinytex/) which has helpers for installing LaTeX functionality.
```r
install.packages('tinytex')
tinytex::install_tinytex()
```
[Bioconductor organization]: https://cloud.docker.com/u/bioconductor/repository/registry-1.docker.io/bioconductor/bioconductor_full