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datacarpentry / genomics-workshop

Genomics Workshop Overview
https://datacarpentry.org/genomics-workshop
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Update to R 4.X #114

Closed ErinBecker closed 1 year ago

ErinBecker commented 4 years ago

@ytakemon recently noted that the AMI has an old version of R installed. Leaving this issue here to remind myself to update to 4.X. Also need to check in with the R Genomics Maintainers to make sure that's not going to break code in the current lesson.

kerchner commented 2 years ago

I'm not entirely sure, but I think upgrading to R 4.2 and beyond is difficult while still on Ubuntu 16 - hence #133

kerchner commented 2 years ago

Also note that R 4.2.1+ may require upgrading RStudio to a 2022.07x version; otherwise the ability to render plots within RStudio may break.

naupaka commented 2 years ago

I think the code used in the current R-genomics lessons should be fine with R 4.2+ since that is what most of us are using to do the development anyway. And since those lessons are still beta I think any fixes we would need to make could be made now with less hassle than later on down the road.

kerchner commented 2 years ago

We have an AMI that we used recently (August 2022) that we would like to contribute. Starting from the original AMI, this AMI contains updates to the version of Ubuntu (I think to 20? Maybe 22? I need to double check) as well as the version of R to 4.2.1 and RStudio server. Hoping to tidy that up and push a pull request here with a change to the AMI id and other associated changes, which may include key screenshots etc. Let me know if that sounds like it would be useful.

naupaka commented 2 years ago

Speaking for myself I think that would be great.

kerchner commented 2 years ago

Awesome, we (myself, @cgaylord-gwu, and @aklwong) will plan to move this forward.

naupaka commented 2 years ago

I think at the moment the Carpentries admin folks have to spin up AWS instances for the workshops manually, so they should be in the loop on any changes. cc @ErinBecker

kerchner commented 2 years ago

That would also drive the choice of pull request reviewers for this one

tobyhodges commented 2 years ago

Thanks @kerchner this sounds like it would be really helpful. If you can provide an AMI, the Core Team will be happy to try to use it to spin up an AWS instance. We could then share that with @naupaka and/or any of the other R Genomics Maintainers who are interested in helping out, so that they can test out the code examples in the lesson?

kerchner commented 1 year ago

Great idea @tobyhodges, we hope to have an AMI to share with you very soon.

kerchner commented 1 year ago

@tobyhodges @naupaka I've created an AMI that I think is ready for the Core Team to test. The AMI id is ami-04dd77cd58b3ec654 (in the N. Virginia region) and it's entitled Data Carpentry Genomics with R 4.2

The AMI includes the following updates:

The newer versions of the command-line tools should be equally available for Mac/Windows users as they are for Linux, since they're all installed via conda.

Once the Core Team has had a chance to test, then I would be glad to create a pull request with updated screenshots and command-line output as needed, and/or we can collaborate on a branch.

naupaka commented 1 year ago

Thanks! Tagging @JasonJWilliamsNY @ytakemon @poterlowicz-lab (the other R-genomics maintainers) so they're in the loop on this as well.

crazyhottommy commented 1 year ago

Thank you! The genomics CAC committee @datacarpentry/curriculum-advisors-genomics (https://github.com/orgs/datacarpentry/teams/curriculum-advisors-genomics) met today and approved the usage of this new AMI.

The related issues are: https://github.com/datacarpentry/genomics-workshop/pull/135 https://github.com/datacarpentry/genomics-workshop/issues/133

kerchner commented 1 year ago

Thanks @crazyhottommy! I'll start putting together a branch/PR with any needed updates to the lesson pages, so that they match what learners will see when using the new AMI.

ErinBecker commented 1 year ago

@kerchner and @datacarpentry/curriculum-advisors-genomics - I cannot tell you how excited I am to see this group moving forward independently to update the AMI. Absolutely amazing work team! Thank you!!

twrightsman commented 1 year ago

This seems solved due to the merge of https://github.com/datacarpentry/genomics-workshop/pull/136.