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 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
Github development link for bioconductor_full
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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.
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Quick start up to start your analysis with all the Bioconductor packages if needed.
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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.
This document assumes you have docker installed. Please check installation if you have more questions regarding this.
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Start docker on your machine.
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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:develor
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
biocuserdocker run \ -it \ --user bioc \ -v ~/host-site-library:/usr/local/lib/R/host-site-library \ bioconductor/bioconductor_full:devel \ RNOTE: The path
/usr/local/lib/R/host-site-libraryis mapped to.libPaths()in R. So, when R is started, all the libraries in the host directory,host-site-libraryare available to R. It is stored on your machine mounted from the volume you fill in place ofhost-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.
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To start the docker image in deamon mode, i.e, have the container running in the background use the
-doption.sudo docker run -it \ -d \ -v host-site-library:/usr/local/lib/R/host-site-library \ --entrypoint /bin/bash \ bioconductor/bioconductor_full:develThis 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 psTo attach to a container which is running in the background
docker exec -it <container_id> bashNOTE: You can replace
bashwith R to start R directly in the container.docker exec -it <container_id> 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:8788docker 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
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xps
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Rmpi
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ccfindR
For more information on the issues for this image, please check
issues.md
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
Install the tinytex package (https://yihui.name/tinytex/) which has helpers for installing LaTeX functionality.
install.packages('tinytex')
tinytex::install_tinytex()