-
Notifications
You must be signed in to change notification settings - Fork 206
Issues/3466 Move away from Gitpod #3569
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
base: dev
Are you sure you want to change the base?
Conversation
…tools into issues/3466-gitpod
…r. Update postCreateCommand to match context
Note: This still uses (a newer) gitpod base image and thus also the |
Codecov ReportAll modified and coverable lines are covered by tests ✅
☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
Bit late to the party here, but note that we went through this process when switching to Devcontainers for the Nextflow Training. In the end we went all-in on the devcontainer spec and stopped thinking about base images entirely. See the current Devcontainer spec: https://github.com/nextflow-io/training/blob/master/.devcontainer/codespaces-dev/devcontainer.json
I'm not sure that we need anything in the devcontainer image that we haven't already sorted in the training image? We already have Nextflow, conda, nf-core/tools etc etc. The simplest approach would be to forget about image entirely and just use this devcontainer spec file with the training base image but mounting a different repo / workdir. If the image being called "training" feels off then we could always move that. Feels more sensible to share effort on the setup there rather than reinventing the wheel though.. |
@ewels Yep, devcontainer Just using the devcontainer from nextflow.io/training would not install the most recent version of tools after a merge, which is the purpose of this exercise, no? But we can use their base image and reinstall tool with dev dependencies and |
Our image for use with devcontainer is now based on The devcontainer.Dockerfile sets up the image for use with the non-root user If we don't need the unprivileged user (the tutorial image just uses |
any update on this? I keep pointing people to codespaces and then the run into docker-in-docker issues... |
I was messing around using pixi in a container to install needed tools. Seems to work OK. I haven't got it fluid yet though. https://github.com/mahesh-panchal/Nextflow_sandbox Feel free to play around. Just FYI. |
# docker build . -t devcontainer:local -f nf_core/devcontainer/devcontainer.Dockerfile | ||
|
||
# Uses mcr.microsoft.com/devcontainers/base:ubuntu | ||
FROM ghcr.io/nextflow-io/training:latest |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
pin the version!
Description
Addresses the suggestions in issue 3466 to move away from gitpod and towards devcontainer for Github codespaces.
PR checklist
CHANGELOG.md
is updateddocs
is updated