Updating Document Pages for Qiime 2 Plugin(s) (GitHub Pages)

Developer Discussion
1

Hello,

I help update and maintain a GitHub Pages repository which documents how to install, update, and use a number of plugins I work on. I recently pushed some changes to the repository, but the changes are not reflected when I visit the webpage. I see, in the past, there was a GitHub Action called "pages build and deployment" run by the "github-pages" bot. I am wondering is anyone has insight to how I can run this action again, or of a different approach I can/should take to update the documentation webpage?

2

Hello Asa,

Here is an example of GItHub Action (and repo) for automatically building docs: https://github.com/bioinf-mcb/Metagenomic-DeepFRI/blob/main/.github/workflows/build_docs.yml

Cheers
V

1 Like
3

Hi @crusher083,

Thank you for sharing this link. I was able to use the workflow and mend it to my needs; however, part of my make process uses qiime2.sdk to create citation, so I need a way to make Qiime2 part of the environment for the workflow. I was wondering if the "environment.yml" in the repo you shared would help with this, or if I would need have the workflow manually install Anaconda and then Qiime2 at runtime?

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4

Hi @asah,

I saw your other post, so this may be redundant - but your method of creating and activating a conda environment that contains the correct packages for your needs (i.e. qiime2, etc) is the right way to go about this. Here's an example from one of our Github workflows that utilizes an environment file in order to activate and use qiime2:

Cheers :lizard: