[EuroBioC2024] Package demo for EuroBioC2024

[bioc-workshop-dev]

DO NOT INCLUDE REQUESTS IN THE FIRST COMMENT.
PLEASE POST THIS TEMPLATE UNCHANGED THEN FOLLOW ITS INSTRUCTIONS IN A NEW
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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): September 05, 2024 - September 05, 2024

Workshop Start Time (approx.): 09:45

[bioc-workshop-dev]

READ ONLY: DO NOT EDIT ## /request id="eurobioc2024isee" title="Package demo for EuroBioC2024" description="This package provides the environment and materials for the package demo at the European Bioconductor Meeting 2024" section="EuroBioC2024" startfile="README.md" source="https://github.com/iSEE/iSEEDemoEuroBioC2024" docker="ghcr.io/isee/iseedemoeurobioc2024:latest" pkglist="iSEE,iSEEde,iSEEhex,iSEEhub,iSEEindex,iSEEpathways,iSEEu,knitr,rmarkdown,pkgdown,BiocStyle,scRNAseq,scater" vignettes="vignettes/workshop_isee_extension.Rmd"

[almahmoud]

/request id="eurobioc2024isee" title="Package demo: iSEE" description="Interactive SummarizedExperiment Explorer" section="EuroBioC2024" source="https://github.com/iSEE/iSEEDemoEuroBioC2024" docker="ghcr.io/isee/iseedemoeurobioc2024:latest" vignettes="vignettes/workshop_isee_extension.Rmd" startfile="vignettes/workshop_isee_extension.Rmd"

[almahmoud]

AUTO-GENERATED RESPONSE
Your request has been received and has passed initial screening. ✨

Below are the detected values:

id='eurobioc2024isee'
title='Package demo: iSEE'
description='Interactive SummarizedExperiment Explorer'
section='EuroBioC2024'
source='https://github.com/iSEE/iSEEDemoEuroBioC2024'
docker='ghcr.io/isee/iseedemoeurobioc2024:latest'
port='8787'
command='echo "setwd(\"/home/rstudio\"); setHook(\"rstudio.sessionInit\", function(newSession) { if (newSession) rstudioapi::filesPaneNavigate(getwd()) }, action = \"append\")" > /home/rstudio/.Rprofile; /init'
pkglist=''
vignettes='vignettes/workshop_isee_extension.Rmd'

If these are as expected, no further action is needed at this time. Please wait for an admin's response.
If any changes are needed, please re-run the /request action with desired values.

[almahmoud]

@kevinrue I removed pkglist="iSEE,iSEEde,iSEEhex,iSEEhub,iSEEindex,iSEEpathways,iSEEu,knitr,rmarkdown,pkgdown,BiocStyle,scRNAseq,scater" or it will create a new container image trying to install the packages on top of your container from the template repo. They should be handled by the DESCRIPTION file in the template repo already so I don't think they are necessary. pkglist is generally used to have a container over bioconductor base container without making a repository. Lmk if I am missing something and/or you think otherwise.

[almahmoud]

/test id="eurobioc2024isee" title="Package demo: iSEE" description="Interactive SummarizedExperiment Explorer" section="EuroBioC2024" source="https://github.com/iSEE/iSEEDemoEuroBioC2024" docker="ghcr.io/isee/iseedemoeurobioc2024:latest" vignettes="vignettes/workshop_isee_extension.Rmd" startfile="vignettes/workshop_isee_extension.Rmd"

[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 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. ✨
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.

[kevinrue]

Makes sense. Thanks!

[almahmoud]

/test id="eurobioc2024isee" title="Package demo: iSEE" description="Interactive SummarizedExperiment Explorer" section="EuroBioC2024" source="https://github.com/iSEE/iSEEDemoEuroBioC2024" docker="ghcr.io/isee/iseedemoeurobioc2024:latest" startfile="vignettes/workshop_isee_extension.Rmd"

[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. ✨
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.