Update Carpentries Gitpod environment

[mahesh-panchal]

Updates the Gitpod environment for Carpentries training.

TODO

• Install tools for exercises. Which tools need to be installed?
• Which pages should include a Launch in Gitpod button?
• Where is the description on how to use Gitpod?
• Are any additional extensions needed?
• What should the checkout location be?
• What branch should be checked out?

[github-actions]

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🔍 Inspect the changes: https://github.com/carpentries-incubator/workflows-nextflow/compare/md-outputs..md-outputs-PR-159

The following changes were observed in the rendered markdown documents:

 md5sum.txt |  2 +-
 setup.md   | 54 +++++++++++++++++++++++++++++++++++++++---------------
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⏱️ Updated at 2024-08-26 11:09:57 +0000

[ggrimes]

Install tools for exercises. Which tools need to be installed?

The tools in the environment.yml file

https://github.com/carpentries-incubator/workflows-nextflow/blob/main/episodes/data/environment.yml

[mahesh-panchal]

Do you want those pinned versions for a reason or do you just want the tools installed? For example, Nextflow is pinned, but presumably you want the latest version right?

[ggrimes]

You are right , for nextflow, python and nf-core tools non-pinned and for the specific version of the software below.

• salmon=1.5
• fastqc=0.11
• multiqc=1.10

[mahesh-panchal]

Those three tools have been added to the environment.

Do we have a specific branch that should be checked out and where should we include launch buttons?

[ggrimes]

I don't have a specific branch in mind, the site is rendered from the main branch, if there any reason not to use this?

[mahesh-panchal]

The summary and setup describes an nf-training folder, so ideally a user should land directly in this. Gitpod only clones a repository, and it's up to us to define that the folder has the expected layout one makes in a non-Gitpod environment.

[ggrimes]

Is it possible as part of gitpod environment set up to create this directory and move into it or is this not advised?

tasks:
  - init: |
      mkdir -p nf-training  # Create the directory
      cd nf-training        # Change into the directory

[mahesh-panchal]

Yes, it's possible.
My preference though would be to create a clean environment free from distracting files.
But let's start with that. Better something than nothing.

[mahesh-panchal]

Are there any particular extensions required for vscode that you would like?
Live-server is there so users can view the multiqc reports. Directly clicking on a MQC report from the side will open up the html, but one can right click it and view with the live server instead to view the rendered version.

[ggrimes]

ticular extensions required for vscode that you would like?
Live-server is there so users can view the multiqc reports. Directly clicking on a MQC report from the side will open up the html, but one can right click it and view with the live server instead to view the rendered version.

I don't have any any particular extensions in mind as I am able to view rendered html using the environment you have already setup. Would be great if you could put any useful extensions in. Also how does the live server work can it render and display the course website within the gitpod environment?

[mahesh-panchal]

I've already added a task to open the course website in a panel. There's a gp preview command to do this.

The live server works by right-clicking on a html file and selecting open with live-server.