[BioC2024] scIGD workflow demo at BioC2024

[ahmadalajami]

DO NOT INCLUDE REQUESTS IN THE FIRST COMMENT. PLEASE POST THIS TEMPLATE UNCHANGED THEN FOLLOW ITS INSTRUCTIONS IN A NEW COMMENT

General Notes

This repository serves as a mostly automated pipeline for deploying workshops to the Bioconductor Workshop.

Bot Commands

Issues in this repository are monitored to by a bot. All commands need to be written on the first line of the comment, in a single line.

Example Docker Request

/request
  id='tidybioc2023'
  title='Tidy Transcriptomics'
  description='For Single-Cell RNA Sequencing Analyses'
  section='Smorgasbord 2023'
  source='https://github.com/tidytranscriptomics-workshops/bioc2023_tidytranscriptomics'
  docker='ghcr.io/tidytranscriptomics-workshops/bioc2023_tidytranscriptomics:latest'

Note. The example /request is on multiple lines for readability.

Additional Workshop Information

Expected Number of Participants: 30

Workshop Date(s): Juli 25, 2024 - Juli 25, 2024

Workshop Start Time (approx.): 16:00

[ahmadalajami]

READ ONLY: DO NOT EDIT ## /request id="scigdbioc2024" title="scIGD workflow demo at BioC2024" description="This package provides the material for the scIGD workflow demo at BioC2024" section="BioC2024" startfile="README.md" source="https://github.com/ahmadalajami/scIGDWorkflowDemoBioC2024" docker="ghcr.io/ahmadalajami/scigdworkflowdemobioc2024:latest" pkglist="" vignettes=""

[almahmoud]

/test id="scigdbioc2024" title="Package demo: scIGD workflow demo" description="Unraveling Immunogenomic Diversity in Single-Cell Data" section="BioC2024" startfile="vignettes/scIGDWorkflowDemo.Rmd" source="https://github.com/ahmadalajami/scIGDWorkflowDemoBioC2024" docker="ghcr.io/ahmadalajami/scigdworkflowdemobioc2024:latest"

[almahmoud]

@ahmadalajami I updated your startfile to be the vignette instead of README, and the description from the title of the workshop. Please lmk if you would rather they be something else

[almahmoud]

AUTO-GENERATED RESPONSE Action Log Your request has passed initial checks and is being built and/or deployed to the test instance. Please wait further updates.

[almahmoud]

AUTO-GENERATED RESPONSE Action Log Your workshop has been successfully deployed to the test instance. :sparkles: Please test your workshop on the development instance and notify us via comment when you deem it ready for public consumption on the production instance.

[ahmadalajami]

@almahmoud, thanks a lot for your feedback! Re the updates: even better, thank you. Re the test: the 2GB allocated on Galaxy are filling up real quick. When running it locally, it is consuming up to 20GB of memory 🫣 If it is unrealistic to allocate that much, I can go through the vignette on the GitHub page instead of running the code line-by-line. That might even be more time efficient. Let me know what you suggest! Thanks once again for your feedback.

[almahmoud]

I do think 20 Gb of memory is too much, as it would not scale well to dozens of participants, especially as other workshops are also running. If you want to try and present live but from your laptop, and have participants follow along doing the same, email conference@bioconductor.org and let them know, they can also accommodate for that

[ahmadalajami]

Totally understandable. What would be the max one could be allocated? Just to see if I can manage to scale it down. If not, I would send an email as suggested.

[almahmoud]

Default is currently 1 Gb reserved, 2 Gb max. I think I can scale up to maybe 5 Gb limit, 3 Gb reserved, more than that I think would be hard to scale for everyone

[ahmadalajami]

Got it. I think we can keep the cloud instance to whoever wanna have a look at it (and because it looks cool 😁). I emailed the team, informing them that I would present/run things locally. Thanks for all the info/help!

[almahmoud]

Hey @ahmadalajami , I think I can give you 5Gb and still scale up to 100+ people, do you think that could be enough to have people be able to follow along?

[ahmadalajami]

@almahmoud, I think so! That would be great - thanks a lot.