[BioC2024] Applying tidy principles to investigating chromatin composition and architecture

[js2264]

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: 40

Workshop Date(s): July 24, 2024 - July 24, 2024

Workshop Start Time (approx.): 02:00

[js2264]

READ ONLY: DO NOT EDIT ## /request id="Bioc2024tidyworkshop" title="Applying tidy principles to investigating chromatin composition and architecture" description="This workshop aims to demonstrate how to use tidyomics methodology to investigate genomic data, including genomic features, genomic interactions and genomic coverage. " section="BioC2024" startfile="README.md" source="https://github.com/js2264/Bioc2024tidyworkshop" docker="ghcr.io/js2264/bioc2024tidyworkshop:latest" pkglist="" vignettes=""

[almahmoud]

/test id="bioc2024tidyworkshop" title="Applying tidy principles to investigating chromatin composition and architecture" description="This workshop aims to demonstrate how to use tidyomics methodology to investigate genomic data, including genomic features, genomic interactions and genomic coverage." section="BioC2024" startfile="vignettes/workshop.Rmd" source="https://github.com/js2264/Bioc2024tidyworkshop" docker="ghcr.io/js2264/bioc2024tidyworkshop:latest" pkglist="" vignettes=""

[almahmoud]

@js2264 I changed the startfile to the vignette in your repository, lmk if you think README.md is better.

[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.

[js2264]

I am hitting some memory issues. I'll work on it and see how to change things. Also, unsure about one thing: what happens if I update the workshop's vignette on my repo? Does it automatically sync with Galaxy? (I'm using the BiuldABiocWorkshop template with automated Docker image etc).

[almahmoud]

Yes, it should sync as long as you're using the template repository's image. Re memory, please let me know if you need higher mem/cpu allocation, I can update it per workshop.

[almahmoud]

@js2264 Any update on needing extra memory/cpu? I can't control how much you get in the github action, but I can mark your workshop to get more on the workshop instance if you let me know. Please test in the workshop instance at workshop.bioconductor.org, and let me know if you need any changes

[js2264]

@almahmoud thanks for keeping in touch, and sorry, I was travelling last week. I've tried to slim down the memory required to run the workshop's chunks all at once. The docker image is now being built, I'll give it a try on the testing instance tomorrow, but it should be ok. I'll let you know!

[js2264]

Checked again with the latest Docker image. Everything runs smoothly. Ready for tomorrow 🎉