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Repository for managing contributions to workshop.bioconductor.org
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[BioC2024] Spatial transcriptomic clustering with BANKSY #83

Open bioc-workshop-dev opened 1 month ago

bioc-workshop-dev commented 1 month ago

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): July 25, 2024 - July 25, 2024

Workshop Start Time (approx.): 14:45

bioc-workshop-dev commented 1 month ago

READ ONLY: DO NOT EDIT ## /request id="banksy07252024" title="Spatial transcriptomic clustering with BANKSY" description="Banksy is an R package that incorporates spatial information to cluster cells in a feature space" section="BioC2024" startfile="README.md" source="https://github.com/prabhakarlab/Banksy" docker=":" pkglist="aricode, data.table, dbscan, SpatialExperiment, SingleCellExperiment, SummarizedExperiment, S4Vectors, stats, matrixStats, mclust, igraph, irlba, leidenAlg (>= 1.1.0), utils, uwot, RcppHungarian" vignettes="https://prabhakarlab.github.io/Banksy/articles/parameter-selection.html, https://prabhakarlab.github.io/Banksy/articles/domain-segment.html, https://prabhakarlab.github.io/Banksy/articles/batch-correction.html, https://prabhakarlab.github.io/Banksy/articles/multi-sample.html"

vipulsinghal02 commented 1 month ago

My apologies, in addition to the packages above, may we also include the following packages? Thanks!

Banksy Seurat scater cowplot ggplot2 scuttle spatialLIBD ExperimentHub harmony, knitr, rmarkdown, pals, scran, testthat (>= 3.0.0), BiocStyle

vipulsinghal02 commented 1 month ago

Hi! Just saw the discussion on slack. Guess we will just do the demo locally on our laptops, but will be using the vignettes from our public git repo. Is there a way to give conference attendees installation instructions for the package before the workshop?

almahmoud commented 1 month ago

@vipulsinghal02 what slack discussion are you referring to? Do you still want it added to the platform? Also, is this a package demo?

vipulsinghal02 commented 1 month ago

Hi Alex,

My apologies for the lack of clarity. This is the discussion I was referring to.

Yes it is a package demo. I thought about it a bit more, and okay yes, lets add us to the platform. Using your cloud platform might be the easiest way after all.

Best, Vipul

almahmoud commented 1 month ago

/test id="banksy07252024" title="Package Demo: Banksy" description="Spatial transcriptomic clustering with BANKSY" section="BioC2024" startfile="vignettes/parameter-selection.Rmd" source="https://github.com/prabhakarlab/Banksy" docker="ghcr.io/bioconductor/bioconductor:3.19" pkglist="prabhakarlab/Banksy" vignettes="vignettes/*"

almahmoud commented 1 month ago

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 commented 1 month ago

AUTO-GENERATED RESPONSE Action Log Your request has been received but is currently failing its deployment on test. If the corresponding /request command has passed with the same parameters, this is likely a bug.

almahmoud commented 1 month ago

/test id="banksy07252024" title="Package Demo: Banksy" description="Spatial transcriptomic clustering with BANKSY" section="BioC2024" startfile="vignettes/parameter-selection.Rmd" source="https://github.com/prabhakarlab/Banksy" docker="ghcr.io/bioconductor/bioconductor:3.19" pkglist="prabhakarlab/Banksy"

almahmoud commented 1 month ago

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 commented 1 month ago

/test id="banksy07252024" title="Package Demo: Banksy" description="Spatial transcriptomic clustering with BANKSY" section="BioC2024" startfile="vignettes/parameter-selection.Rmd" source="https://github.com/prabhakarlab/Banksy" docker="ghcr.io/bioconductor/bioconductor:3.19" pkglist="prabhakarlab/Banksy"

almahmoud commented 1 month ago

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 commented 1 month ago

AUTO-GENERATED RESPONSE Action Log Your request has been received but is currently failing its deployment on test. If the corresponding /request command has passed with the same parameters, this is likely a bug.

almahmoud commented 1 month ago

AUTO-GENERATED RESPONSE Action Log Your request has been received but is currently failing its deployment on test. If the corresponding /request command has passed with the same parameters, this is likely a bug.

almahmoud commented 1 month ago

/test id="banksy07252024" title="Package Demo: Banksy" description="Spatial transcriptomic clustering with BANKSY" section="BioC2024" startfile="vignettes/parameter-selection.Rmd" source="https://github.com/prabhakarlab/Banksy" docker="ghcr.io/bioconductor/bioconductor:3.19" pkglist="prabhakarlab/Banksy"

almahmoud commented 1 month ago

P.S. This workshop is having its image build correctly but failing on push. Can build manually if needed, but trying to fix it to push to Dockerhub if fails to GHCR.io

almahmoud commented 1 month ago

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 commented 1 month ago

AUTO-GENERATED RESPONSE Action Log Your request has been received but is currently failing its deployment on test. If the corresponding /request command has passed with the same parameters, this is likely a bug.

almahmoud commented 1 month ago

/test id="banksy07252024" title="Package Demo: Banksy" description="Spatial transcriptomic clustering with BANKSY" section="BioC2024" startfile="vignettes/parameter-selection.Rmd" source="https://github.com/prabhakarlab/Banksy" docker="ghcr.io/bioconductor/bioconductor:3.19" pkglist="prabhakarlab/Banksy"

almahmoud commented 1 month ago

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 commented 1 month ago

AUTO-GENERATED RESPONSE Action Log Your request has been received but is currently failing its deployment on test. If the corresponding /request command has passed with the same parameters, this is likely a bug.

vipulsinghal02 commented 1 month ago

P.S. This workshop is having its image build correctly but failing on push. Can build manually if needed, but trying to fix it to push to Dockerhub if fails to GHCR.io

Hmm okay. Will keep an eye out for when it’s ready. We will have a local presentation ready to project from our laptop just in case.

Thanks a lot!!

almahmoud commented 1 month ago

I'm not entirely sure why this one gave so much trouble with the automatic tooling compared to others, but will dig into it later. I've added it manually, please test it up on the platform.

vipulsinghal02 commented 1 month ago

Thanks a lot, Alex! Getting on the flight, so will have spotty internet for the next day or so, but will test it whenever I can.

Cheers, Vipul