Updated renv and conda-env-yaml instructions #35
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Merge recent changes from CHTC/recipes main into my own fork of the repo.
… it could help visualize the flow of information.
…-up, and instructions.
…simple environment you want to design a def file directly for.
…xist, and there are no tar.gz file examples I could find in this repo.
| - https://conda.anaconda.org/conda-forge | ||
| - https://repo.anaconda.com/pkgs/main | ||
| - https://repo.anaconda.com/pkgs/r |
Contributor
There was a problem hiding this comment.
Suggested change
| - https://repo.anaconda.com/pkgs/r |
Apologies for unasked for "drive by" PR comments, but as the Anaconda r channel is deprecated and no longer maintained (c.f. https://www.anaconda.com/blog/changes-to-anacondas-r-channel-support) mentioning it at all should probably be avoided in documentation. As mentioned in Anaconda's blog post, conda-forge has rather good coverage of CRAN these days and so between the conda-forge and bioconda channels this should cover all modern use cases.
Author
There was a problem hiding this comment.
That's good to know - I agree we could remove the line mentioning the r channel in the example printout on the documentation to avoid confusion then.
Contributor
|
Sorry for the delay; I'm planning to review this PR today or tomorrow. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Hi CHTC team,
I was working with some students on the
renvandconda-env-yamlfull workflow from their laptops to CHTC, and took on the task to add onto the existing README instructions based on the feedback and questions from students.For the
recipes/software/R/renvworkflow, I added a workflow figure to demonstrate what/how/where files should be located. Students have mentioned that visuals can help. I also added instructions on how to solve the Linux dependencies problem, which were TBD previously (ticket #118430 - thanks @xamberl ). I reformatted the layout and added callout bubbles with extra tips. I added a section linking to the HTC guides/docs for skills mentioned in the readme file.For the
recipes/software/conda/conda-yamlreadme file, I mainly reformatted the readme file and added some more details.In both cases, I added an overview section at the beginning that previews the steps and general concepts. I tried to keep it general not not domain-specific.
I added a folder
docs/to store screenshots/images that are linked in the workflow, but I'm not sure if that follows your stylistic guidelines.Hope this helps in some way! Suggestions welcomed. And thank you for the example recipes and instructions.
Patricia