[Bioc 2023] Package Demo: Statial

[ellispatrick]

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 listen to by a bot. All commands need to be written on the first line of the comment, in a single line, starting with the /command and containing all parameter="value in here" pairs.

Public request

Unless you are a member of the Bioconductor Core team or an administrator of this repository, you can only perform /request commands in this space. Some parameters are universal to all requests and mandatory, namely the Title, Description, Source URL, and Section on the workshop instance. You may request your workshop be added to an existing section, or request a new Section name.
Below is an example of an incomplete request with all mandatory parameters:

/request id="myworkshopuniqueid" title="Bold Text" description="unbolded text next to the title" section="Conference 1996" source="https://github.com/super/repository" 

This request will then need to be completed with an additional 1-2 parameters depending on your source for the workshop.

We currently support 3 types of submissions:

1. docker= parameter for pre-built RStudio containers (such as Orchestra workshops built based on BuildABiocWorkshop)
   Below is an example of a full /request command for a workshop with a pre-built docker container:

/request id="tidybioc2022" title="Tidy Transcriptomics" description="For Single-Cell RNA Sequencing Analyses" section="Smorgasbord 2023" source="https://github.com/tidytranscriptomics-workshops/bioc2022_tidytranscriptomics" docker="ghcr.io/tidytranscriptomics-workshops/bioc2022_tidytranscriptomics:latest"

2. vignettes= parameter for Rmd/qmd workshops.

Note that when any Rmd or qmd files are pulled as part of a request including vignettes, the script will only deploy successfully if the vignettes can successfully render. In the process, all dependencies will be automatically scraped and installed in the resulting container image, making it optional to explicitly mention dependencies.

2. a) In-source vignettes, especially useful for example if your Rmd references other files (eg: images), in which case you should include them in your source repository. Parameter represents a comma-separated list of relative paths (with wildcards accepted) from your source repository. Eg: vignettes="vignettes/*,images/*" will copy all files from your source repository under those two subdirectories.

Below is an example of a full request with in-source vignettes:

/request id="annotation316" title="Genomic Annotation Resources" description="with Bioconductor annotation package" section="Smorgasbord 2023" source="https://github.com/Bioconductor/annotation" vignettes="vignettes/*"

2. b) markdown file urls, in the form of a comma-separated list of URLs. eg: vignettes="https://raw.githubusercontent.com/Bioconductor/annotation/devel/vignettes/Annotation_Resources.Rmd,https://raw.githubusercontent.com/Bioconductor/annotation/devel/vignettes/Annotating_Genomic_Ranges.Rmd". This can especially be useful for people unfamiliar with github, who could write a self-contained Rmd file in RStudio, paste it at https://gist.github.com where single files can be hosted with no directory structure or git operations.

Below is an example of a full request for a url vignette:

/request id="genranges316" title="Annotating Genomic Ranges" description="with Bioconductor annotation package" section="Smorgasbord 2023" source="https://raw.githubusercontent.com/Bioconductor/annotation/devel/vignettes/Annotating_Genomic_Ranges.Rmd" vignettes="https://raw.githubusercontent.com/Bioconductor/annotation/devel/vignettes/Annotating_Genomic_Ranges.Rmd,https://raw.githubusercontent.com/Bioconductor/annotation/devel/vignettes/Annotating_Genomic_Ranges.Rmd"

3. pkglist= which can be used with or without the vignettes= option, in order to add a list of Bioconductor and/or CRAN packages to the resulting auto-built container image for this request. It should be passed as a comma-separated list of package names. eg: pkglist="VariantAnnotation,AnnotationHub,TxDb.Hsapiens.UCSC.hg19.knownGene"

Below is an example of a request to add a package demo

/request id="bsgenome316" title="BSgenome package demo" description="in the latest Bioconductor" section="Package Demos" source="https://github.com/Bioconductor/BSgenome" pkglist="BSgenome"

Every request must contain at least 1 of the 3 listed parameters, in addition to the mandatory parameters listed above.

You may add any comments, information or special requests after the second line, but the first line must contain only the /command and its parameters.

Admin request

Bioconductor Core Team and repository admins will be able to deploy vetted requests to one of two servers. These requests take the same parameters as the /request command, but go through with building and deploying the changes. When the request does not include a docker= parameter, the image building might delay a response by a couple of hours for package-intensive workshops.

The /test command will deploy the instance to our test server, where the requester can verify the aesthetics as well as functionality of the workshop and request any changes.

The /publish command will deploy the final approved workshop to the production instance.

The best way for an admin to populate these requests is copy-paste the last passing full /request command and all parameters from the requester, and replace the /request command with the appropriate deployment directive.

[ellispatrick]

/request id="bioc2023statial" title="Package Demo: Statial" description="Statial: A Bioconductor package for identifying spatially-related changes in cell state" section="BioC 2023" startfile="vignettes/An_introduction_to_Statial.Rmd" vignettes="vignettes/*" keepsource="TRUE" source="https://github.com/SydneyBioX/StatialBioc2023" docker="ghcr.io/sydneybiox/statialbioc2023:latest"

[almahmoud]

AUTO-GENERATED RESPONSE
Your request has been received but is currently failing initial screening.
Please retry your request ensuring all parameters are passed in correctly.

[ellispatrick]

/request id="bioc2023statial" title="Package Demo: Statial" description="Statial: A Bioconductor package for identifying spatially-related changes in cell state" section="BioC 2023" source="https://github.com/SydneyBioX/StatialBioc2023" pkglist="Statial"

[almahmoud]

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

Below are the detected values:

source='bioc2023statial'
title='Package Demo: Statial'
description='Statial: A Bioconductor package for identifying spatially-related changes in cell state'
section='BioC 2023'
source='https://github.com/SydneyBioX/StatialBioc2023'
docker=''
port='8787'
command='echo "setwd(\"/home/rstudio\"); setHook(\"rstudio.sessionInit\", function(newSession) { if (newSession) rstudioapi::filesPaneNavigate(getwd()) }, action = \"append\")" > /home/rstudio/.Rprofile; /init'
pkglist='Statial'
vignettes=''

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]

/test id="bioc2023statial" title="Package Demo: Statial" description="Statial: A Bioconductor package for identifying spatially-related changes in cell state" section="BioC 2023" source="https://github.com/SydneyBioX/StatialBioc2023" pkglist="Statial,SydneyBioX/StatialBioc2023" vignettes="vignettes/*" startfile="vignettes/An_introduction_to_Statial.Rmd"

[almahmoud]

/test id="bioc2023statial" title="Package Demo: Statial" description="Statial: A Bioconductor package for identifying spatially-related changes in cell state" section="BioC 2023" source="https://github.com/SydneyBioX/StatialBioc2023" pkglist="Statial,SydneyBioX/StatialBioc2023" vignettes="vignettes/*" startfile="vignettes/An_introduction_to_Statial.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]

/test id="bioc2023statial" title="Package Demo: Statial" description="Statial: A Bioconductor package for identifying spatially-related changes in cell state" section="BioC 2023" source="https://github.com/SydneyBioX/StatialBioc2023" pkglist="Statial,SydneyBioX/StatialBioc2023" vignettes="vignettes/*" startfile="vignettes/An_introduction_to_Statial.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.

[ellispatrick]

/test id="bioc2023statial" title="Package Demo: Statial" description="Statial: A Bioconductor package for identifying spatially-related changes in cell state" section="BioC 2023" source="https://github.com/SydneyBioX/StatialBioc2023" pkglist="Statial,SydneyBioX/StatialBioc2023" vignettes="vignettes/*" startfile="vignettes/An_introduction_to_Statial.Rmd"

[ellispatrick]

Hi @almahmoud ,
How do I push changes to the test instance?
Thanks,
E

[almahmoud]

You do not have permission to do so, and I already cached the instances on the nodes, so ideally we wouldn't restart everything the day before the conference for a change. If it is ABSOLUTELY NECESSARY, let me know and I will try to do it I am doing it now before it gets later

[almahmoud]

/test id="bioc2023statial" title="Package Demo: Statial" description="Statial: A Bioconductor package for identifying spatially-related changes in cell state" section="BioC 2023" source="https://github.com/SydneyBioX/StatialBioc2023" pkglist="Statial,SydneyBioX/StatialBioc2023" vignettes="./vignettes/*" startfile="vignettes/An_introduction_to_Statial.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.

[ellispatrick]

Hi @almahmoud,

So sorry, we ran into a few issues and it took us longer to pull together than we had expected.

I am currently getting the following when I try to launch the test instance, have I done something wrong?

bioc2023statial | stopped | 5 minutes ago | 5 minutes ago

[ellispatrick]

Don't worry, it is working now and we are happy with it :)
Thanks for all of your help and sorry for the last minute rush.

[ellispatrick]

Hi @almahmoud ,
I'm just confirming if the workshop is currently accessible to the participants today?
Thanks,
Ellis

[almahmoud]

It should be. If it is not, let me know ASAP what issues you experience. The caching might not work (depends on the node ends up being selected) so the startup might take a minute, but I am freezing any changes to not have last minute downtime.

[ellispatrick]

Works well thank you, I just wasn't sure if what I was seeing is what someone else would see.

Thank you again for all of your last minute help.

[almahmoud]

/test id="bioc2023statial" title="Package Demo: Statial" description="a Bioconductor package for identifying spatially-related changes in cell state" section="BioC 2023" source="https://github.com/SydneyBioX/StatialBioc2023" pkglist="Statial,SydneyBioX/StatialBioc2023" startfile="vignettes/An_introduction_to_Statial.Rmd" docker="ghcr.io/sydneybiox/statialbioc2023:latest"

[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 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]

/test id="bioc2023statial" title="Package Demo: Statial" description="a Bioconductor package for identifying spatially-related changes in cell state" section="BioC 2023" source="https://github.com/SydneyBioX/StatialBioc2023" startfile="vignettes/An_introduction_to_Statial.Rmd" docker="ghcr.io/sydneybiox/statialbioc2023:latest"

[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 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]

/test id="bioc2023statial" title="Package Demo: Statial" description="a Bioconductor package for identifying spatially-related changes in cell state" section="BioC 2023" source="https://github.com/SydneyBioX/StatialBioc2023" startfile="vignettes/An_introduction_to_Statial.Rmd" docker="ghcr.io/sydneybiox/statialbioc2023:latest"

[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 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]

/test id="bioc2023statial" title="Package Demo: Statial" description="a Bioconductor package for identifying spatially-related changes in cell state" section="BioC 2023" source="https://github.com/SydneyBioX/StatialBioc2023" startfile="vignettes/An_introduction_to_Statial.Rmd" docker="ghcr.io/sydneybiox/statialbioc2023:latest"

[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.