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Add docker-compose documentation to Docker help.
- The Deprecation notice has been moved to the bottom of the page as it's quite old now. - TODO: There should be a way to sync the README of the bioconductor_docker github page to the website.
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|---|---|---|
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@@ -17,19 +17,20 @@ or [Microsoft Azure Container Instances](https://azure.microsoft.com/en-us/servi | |
| - [Why Use Containers](#intro) | ||
| * [Goals for new containers](#goals) | ||
| - [Current Containers](#current) | ||
| - [Deprecation Notice](#deprecation) | ||
| * [Legacy Containers](#legacy) | ||
| * [Reason for deprecation](#reason) | ||
| * [Reporting issues](#issues) | ||
| - [Using Containers](#usage) | ||
| * [Running Containers](#running) | ||
| * [Mounting Additional Volume](#mounting) | ||
| * [Using docker-compose](#dockercompose) | ||
| - [Modifying Image Container](#modify) | ||
| - [Singularity](#singularity) | ||
| - [Microsoft Azure Container Instances](#msft) | ||
| * [Using containers hosted on Microsoft Container Registry](#mcr) | ||
| * [Use Azure Container Instances to run bioconductor images on-demand on Azure](#aci) | ||
| - [How to contribute](#contribute) | ||
| - [Deprecation Notice](#deprecation) | ||
| * [Legacy Containers](#legacy) | ||
| * [Reason for deprecation](#reason) | ||
| * [Reporting issues](#issues) | ||
| - [Acknowledgements](#acknowledgements) | ||
|
|
||
| <a name="quickstart"></a> | ||
|
|
@@ -123,97 +124,6 @@ For each supported version of Bioconductor, we provide | |
| Bioconductor's Docker images are stored in [Docker Hub](https://hub.docker.com/u/bioconductor/); | ||
| the source Dockerfile(s) are in [Github](https://github.com/Bioconductor/bioconductor_docker). | ||
|
|
||
| <a name="deprecation"></a> | ||
| ## Deprecation Notice | ||
|
|
||
| For previous users of docker containers for Bioconductor, please note | ||
| that we are deprecating the following images. These images were | ||
| maintained by Bioconductor Core, and also the community. | ||
|
|
||
| <a name="legacy"></a> | ||
| ### Legacy Containers | ||
|
|
||
| These images are NO LONGER MAINTAINED and updated. They will however | ||
| be available to use should a user choose. They are not | ||
| supported anymore by the Bioconductor Core team. | ||
|
|
||
| Bioconductor Core Team: [email protected] | ||
|
|
||
| * [bioconductor/devel_base2](https://hub.docker.com/r/bioconductor/devel_base2/) | ||
| * [bioconductor/devel_core2](https://hub.docker.com/r/bioconductor/devel_core2/) | ||
| * [bioconductor/release_base2](https://hub.docker.com/r/bioconductor/release_base2/) | ||
| * [bioconductor/release_core2](https://hub.docker.com/r/bioconductor/release_core2/) | ||
|
|
||
| Steffen Neumann: [email protected], Maintained as part of the "PhenoMeNal, funded by Horizon2020 grant 654241" | ||
|
|
||
| * [bioconductor/devel_protmetcore2](https://hub.docker.com/r/bioconductor/devel_protmetcore2/) | ||
| * [bioconductor/devel_metabolomics2](https://hub.docker.com/r/bioconductor/devel_metabolomics2/) | ||
| * [bioconductor/release_protmetcore2](https://hub.docker.com/r/bioconductor/release_protmetcore2/) | ||
| * [bioconductor/release_metabolomics2](https://hub.docker.com/r/bioconductor/release_metabolomics2/) | ||
|
|
||
| Laurent Gatto: [email protected] | ||
|
|
||
| * [bioconductor/devel_mscore2](https://hub.docker.com/r/bioconductor/devel_mscore2/) | ||
| * [bioconductor/devel_protcore2](https://hub.docker.com/r/bioconductor/devel_protcore2/) | ||
| * [bioconductor/devel_proteomics2](https://hub.docker.com/r/bioconductor/devel_proteomics2/) | ||
| * [bioconductor/release_mscore2](https://hub.docker.com/r/bioconductor/release_mscore2/) | ||
| * [bioconductor/release_protcore2](https://hub.docker.com/r/bioconductor/release_protcore2/) | ||
| * [bioconductor/release_proteomics2](https://hub.docker.com/r/bioconductor/release_proteomics2/) | ||
|
|
||
| RGLab: [email protected] | ||
|
|
||
| * [bioconductor/devel_cytometry2](https://hub.docker.com/r/bioconductor/devel_cytometry2/) | ||
| * [bioconductor/release_cytometry2](https://hub.docker.com/r/bioconductor/release_cytometry2/) | ||
|
|
||
| First iteration containers | ||
|
|
||
| * bioconductor/devel_base | ||
| * bioconductor/devel_core | ||
| * bioconductor/devel_flow | ||
| * bioconductor/devel_microarray | ||
| * bioconductor/devel_proteomics | ||
| * bioconductor/devel_sequencing | ||
| * bioconductor/devel_metabolomics | ||
| * bioconductor/release_base | ||
| * bioconductor/release_core | ||
| * bioconductor/release_flow | ||
| * bioconductor/release_microarray | ||
| * bioconductor/release_proteomics | ||
| * bioconductor/release_sequencing | ||
| * bioconductor/release_metabolomics | ||
|
|
||
| <a name="reason"></a> | ||
| ### Reason for deprecation | ||
|
|
||
| The new Bioconductor Docker image `bioconductor/bioconductor_docker` | ||
| makes it possible to easily install any package the user chooses since | ||
| all the system dependencies are built in to this new image. The | ||
| previous images did not have all the system dependencies built in to | ||
| the image. The new installation of packages can be done with, | ||
|
|
||
| BiocManager::install(c("package_name", "package_name")) | ||
|
|
||
| Other reasons for deprecation: | ||
|
|
||
| - the chain of inheritance of Docker images was too complex and hard | ||
| to maintain. | ||
|
|
||
| - Hard to extend because there were multiple flavors of images. | ||
|
|
||
| - Naming convention was making things harder to use. | ||
|
|
||
| - Images which were not maintained were not deprecated. | ||
|
|
||
| <a name="issues"></a> | ||
| ### Reporting Issues | ||
|
|
||
| Please report issues with the new set of images on [GitHub Issues](https://github.com/Bioconductor/bioconductor_docker/issues) or | ||
| the [Bioc-devel](mailto:[email protected]) mailing list. | ||
|
|
||
| These issues can be questions about anything related to this piece of | ||
| software such as, usage, extending Docker images, enhancements, and | ||
| bug reports. | ||
|
|
||
| <a name="usage"></a> | ||
| ## Using the containers | ||
|
|
||
|
|
@@ -350,6 +260,68 @@ package would be available for use. | |
| -p 8787:8787 \ | ||
| bioconductor/bioconductor_docker:devel | ||
|
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||
| <a name="dockercompose"></a> | ||
|
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||
| ### Using docker-compose | ||
|
|
||
| To run the docker-compose file `docker-compose.yaml` from the same | ||
| directory, | ||
|
|
||
| ``` | ||
| docker-compose up | ||
| ``` | ||
|
|
||
| Using `docker-compose`, the user can launch the image with a single | ||
| command. The RStudio image is launched at `http://localhost:8787`. | ||
|
|
||
| The `docker-composer.yaml` includes settings so that the user doesn't | ||
| have to worry about setting the port, password (default is `bioc`), or | ||
| the volume to save libraries. | ||
|
|
||
| The library path, where all the packages are installed are | ||
| automatically configured to use the volume | ||
| `$HOME/R/bioconductor_docker/<bioconductor_version>`, in the case of | ||
| the Bioconductor version 3.13, it would be | ||
| `$HOME/R/bioconductor_docker/3.13`. This location is mounted on to the | ||
| path, `/usr/local/lib/R/host-site-library`, which is the first value | ||
| in your search path for packages if you check `.libPaths()`. | ||
|
|
||
| When the user starts the docker image using `docker-compose`, it will | ||
| recognize previously mounted libraries with the apprpriate | ||
| bioconductor version, and save users time reinstalling the previously | ||
| installed packages. | ||
|
|
||
| To add another volume for data, it's possible to modify the | ||
| `docker-compose.yml` to include another volume, so all the data is | ||
| stored in the same location as well. | ||
|
|
||
| ``` | ||
| volumes: | ||
| - ${HOME}/R/bioconductor_docker/3.13:/usr/local/lib/R/host-site-library | ||
| - ${HOME}/R/data:/home/rstudio | ||
| ``` | ||
|
|
||
|
|
||
| To run in the background, use the `-d` or `--detach` flag, | ||
|
|
||
| ``` | ||
| docker-compose up -d | ||
| ``` | ||
|
|
||
| If the image is run in a detached state, the `container-name` can be | ||
| used to exec into the terminal if the user wishes `root` access in a | ||
| terminal, without using RStudio. | ||
|
|
||
| Within the `root` user, additional system dependencies can be | ||
| installed to make the image fit the needs of the user. | ||
|
|
||
| ``` | ||
| docker exec -it bioc-3.13 bash | ||
| ``` | ||
|
|
||
| For more information on how to use `docker-compose`, use the | ||
| [official docker-compose reference](https://docs.docker.com/compose/reference/up/). | ||
|
|
||
| <p class="back_to_top">[ <a href="#top">Back to top</a> ]</p> | ||
|
|
||
| <a name="modify"></a> | ||
|
|
@@ -738,6 +710,97 @@ community members can contribute images | |
|
|
||
| link: https://github.com/Bioconductor/bioconductor_docker/blob/master/best_practices.md | ||
|
|
||
| <a name="acknowledgements"></a> | ||
| ## Deprecation Notice | ||
|
|
||
| For previous users of docker containers for Bioconductor, please note | ||
| that we are deprecating the following images. These images were | ||
| maintained by Bioconductor Core, and also the community. | ||
|
|
||
| <a name="legacy"></a> | ||
| ### Legacy Containers | ||
|
|
||
| These images are NO LONGER MAINTAINED and updated. They will however | ||
| be available to use should a user choose. They are not | ||
| supported anymore by the Bioconductor Core team. | ||
|
|
||
| Bioconductor Core Team: [email protected] | ||
|
|
||
| * [bioconductor/devel_base2](https://hub.docker.com/r/bioconductor/devel_base2/) | ||
| * [bioconductor/devel_core2](https://hub.docker.com/r/bioconductor/devel_core2/) | ||
| * [bioconductor/release_base2](https://hub.docker.com/r/bioconductor/release_base2/) | ||
| * [bioconductor/release_core2](https://hub.docker.com/r/bioconductor/release_core2/) | ||
|
|
||
| Steffen Neumann: [email protected], Maintained as part of the "PhenoMeNal, funded by Horizon2020 grant 654241" | ||
|
|
||
| * [bioconductor/devel_protmetcore2](https://hub.docker.com/r/bioconductor/devel_protmetcore2/) | ||
| * [bioconductor/devel_metabolomics2](https://hub.docker.com/r/bioconductor/devel_metabolomics2/) | ||
| * [bioconductor/release_protmetcore2](https://hub.docker.com/r/bioconductor/release_protmetcore2/) | ||
| * [bioconductor/release_metabolomics2](https://hub.docker.com/r/bioconductor/release_metabolomics2/) | ||
|
|
||
| Laurent Gatto: [email protected] | ||
|
|
||
| * [bioconductor/devel_mscore2](https://hub.docker.com/r/bioconductor/devel_mscore2/) | ||
| * [bioconductor/devel_protcore2](https://hub.docker.com/r/bioconductor/devel_protcore2/) | ||
| * [bioconductor/devel_proteomics2](https://hub.docker.com/r/bioconductor/devel_proteomics2/) | ||
| * [bioconductor/release_mscore2](https://hub.docker.com/r/bioconductor/release_mscore2/) | ||
| * [bioconductor/release_protcore2](https://hub.docker.com/r/bioconductor/release_protcore2/) | ||
| * [bioconductor/release_proteomics2](https://hub.docker.com/r/bioconductor/release_proteomics2/) | ||
|
|
||
| RGLab: [email protected] | ||
|
|
||
| * [bioconductor/devel_cytometry2](https://hub.docker.com/r/bioconductor/devel_cytometry2/) | ||
| * [bioconductor/release_cytometry2](https://hub.docker.com/r/bioconductor/release_cytometry2/) | ||
|
|
||
| First iteration containers | ||
|
|
||
| * bioconductor/devel_base | ||
| * bioconductor/devel_core | ||
| * bioconductor/devel_flow | ||
| * bioconductor/devel_microarray | ||
| * bioconductor/devel_proteomics | ||
| * bioconductor/devel_sequencing | ||
| * bioconductor/devel_metabolomics | ||
| * bioconductor/release_base | ||
| * bioconductor/release_core | ||
| * bioconductor/release_flow | ||
| * bioconductor/release_microarray | ||
| * bioconductor/release_proteomics | ||
| * bioconductor/release_sequencing | ||
| * bioconductor/release_metabolomics | ||
|
|
||
| <a name="reason"></a> | ||
| ### Reason for deprecation | ||
|
|
||
| The new Bioconductor Docker image `bioconductor/bioconductor_docker` | ||
| makes it possible to easily install any package the user chooses since | ||
| all the system dependencies are built in to this new image. The | ||
| previous images did not have all the system dependencies built in to | ||
| the image. The new installation of packages can be done with, | ||
|
|
||
| BiocManager::install(c("package_name", "package_name")) | ||
|
|
||
| Other reasons for deprecation: | ||
|
|
||
| - the chain of inheritance of Docker images was too complex and hard | ||
| to maintain. | ||
|
|
||
| - Hard to extend because there were multiple flavors of images. | ||
|
|
||
| - Naming convention was making things harder to use. | ||
|
|
||
| - Images which were not maintained were not deprecated. | ||
|
|
||
| <a name="issues"></a> | ||
| ### Reporting Issues | ||
|
|
||
| Please report issues with the new set of images on [GitHub Issues](https://github.com/Bioconductor/bioconductor_docker/issues) or | ||
| the [Bioc-devel](mailto:[email protected]) mailing list. | ||
|
|
||
| These issues can be questions about anything related to this piece of | ||
| software such as, usage, extending Docker images, enhancements, and | ||
| bug reports. | ||
|
|
||
| <a name="acknowledgements"></a> | ||
| ## Acknowledgements | ||
|
|
||
|
|
||