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Bioconductor / workshop-contributions

Repository for managing contributions to workshop.bioconductor.org
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[EuroBioC2024] Package demo for EuroBioC2024 #81

Open bioc-workshop-dev opened 3 months ago

bioc-workshop-dev commented 3 months 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): September 05, 2024 - September 05, 2024

Workshop Start Time (approx.): 09:45

bioc-workshop-dev commented 3 months ago

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 commented 3 months ago

/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 commented 3 months ago

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

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 commented 3 months ago

@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 commented 3 months ago

/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 commented 3 months 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 3 months 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 3 months ago

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.

kevinrue commented 3 months ago

Makes sense. Thanks!

almahmoud commented 3 months ago

/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 commented 3 months 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 3 months ago

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.