Docs: using docker images #538
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Generally I think this looks good. I'm on board with the level of detail, but I do think at least some minimal example of the docker run command would be helpful with notes that link you to the Docker docs so contributors can customize to their needs.
Also, I agree that using Docker on LSfR is something that can be added later. I may actually add that in the LSfR section rather than the Docker section and link to it from these pages.
| 4. You can now use the image to run code from the analysis module using [the `docker run` command](https://docs.docker.com/reference/cli/docker/container/run/) from a terminal. | ||
| - The analysis module's `README.md` file should contain documentation for what command(s) you need to issue to [run the module](../../contributing-to-analyses/analysis-modules/running-a-module.md). | ||
| - You will also need to [mount a volume](https://docs.docker.com/storage/volumes/) as part of your command to ensure that the Docker container has access to all files needed, including any data files. | ||
| - Note that containers for [images based on `bioconductor/r-ver`](./docker-images.md#r-based-images) can also be run in the browser as interactive RStudio Server sessions, [as described in the Bioconductor documentation](https://www.bioconductor.org/help/docker/). |
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I'm wondering if it might make sense to show a minimal example of what running the image with mounting a volume looks like? I know we are assuming previous experience, but I do think it could be helpful to provide an example in one place. Something like:
docker run -it --mount type=bind,source="path to local files",target="path to container files" <module-name>:latest
If you have a different preferred way of running a container then we could use that too, but I think an example could be helpful.
Co-authored-by: Ally Hawkins <[email protected]>
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This should now be ready for another look! In addition to other responses to review, I've expanded the discussion of using |
Co-authored-by: Ally Hawkins <[email protected]>
sjspielman
merged commit 6818678
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AlexsLemonade:reproducibility-docs
Closes #496
This PR adds documentation for using Docker images. To start, I stayed fairly thin on details for how to use Docker in the first place, under the assumption that contributors who actually want to pull images and run in containers have a sense of what they're doing already. I included a note to this end, and I also added a couple more Docker resources (links from training materials).
Let me know if there are any particular details that I glossed over which you think I should mention and/or emphasize more. For example, should I say more about
docker runflags or volumes?One item that this PR does not cover but we should probably open an issue for is running docker images in LSfR, which may be necessary for certain modules depending on their compute needs. Do you agree we should circle back to this?