BiocWorkshopSubmit

Introduction & Installation

The BiocWorkshopSubmit package is a Shiny app that allows users to submit Bioconductor workshops to the Bioconductor Workshop website via the workshop contributions repository on GitHub. The app is designed to be used as a standalone local app with a particular setup.

The package is only available on GitHub and can be installed with the following command:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Bioconductor/BiocWorkshopSubmit")

Setup

Workshop submitters should include the following files in their workshop:

A DESCRIPTION file with the following fields:

• Title: A title for the workshop
• Description: A short description of the workshop
• URL: A URL to the workshop repository from either GHCR or Docker Hub

Note. The container should be built using the Dockerfile that is included in the example BuildABiocWorkshop repository. It can either point to docker.io or ghcr.io.

The DESCRIPTION file should be used to indicate what packages are needed for the workshop. The DESCRIPTION file should also be used to indicate what version of R is needed for the workshop.

Once the container is built, the workshop should be tested locally to ensure that it works as expected. The workshop should be tested (preferably) on the latest release version of R and Bioconductor.

Creating a GH Issue

The app will create a GitHub issue in the the workshop-contributions repository. Submitters should generate a fine-grained personal access token via GitHub https://github.com/settings/tokens. The token should have the public_repo scope. The token should be saved with gitcreds::gitcreds_set(). Once the token is saved, the app will use it to create the issue.

Usage

The app can be launched with the following command:

BiocWorkshopSubmit::BiocWorkshopSubmit()

BiocWorkshopSubmit Interface

The app will prompt the presenter to submit the following information:

• GitHub repository: The GitHub repository where the workshop contents are hosted.
• Workshop ID: A unique identifier for the workshop, e.g., tidybioc2023.
• Section: The section that corresponds to the group of workshops for a particular event (if any; e.g., Bioc2023).
• Start File: The file that should be open when the user logs in to the workshop instance.
• Container Tag: The tag for the container that should be used for the workshop (typically, latest).

The workshop presenter will be able to auto-populate the fields in the app by clicking the Populate button. The app will use the DESCRIPTION file on GitHub to update the fields in the app.

Additional Information

Additional Information

Workshop presenters can also provide additional information regarding the size, start time, and date of the workshop. This information will be used to allocate resources for the workshop on the Bioconductor Workshop website.

• Workshop Date: The date interval of the workshop event.
• Workshop Start Time (24h format): The start time of the workshop event in Eastern US time.
• Expected Number of Participants: The expected number of participants for the workshop.

Submitting the Workshop

After the details of the workshop have been entered, the workshop presenter will be able to click the red Submit button to submit the workshop to the workshop-contributions repository. The app will create a GitHub issue in the workshop-contributions repository with the details of the workshop. Please monitor the issue for any comments from the Bioconductor team.

Thank you for your contribution to the Bioconductor Workshop website!

Example Workshops

The following workshops have been submitted to the Bioconductor Workshop:

• MultiAssayWorkshop: https://github.com/waldronlab/MultiAssayWorkshop
• ISMB.OSCA: https://github.com/Bioconductor/ISMB.OSCA

Feel free to refer to these workshops as examples of how to structure the workshop package for submission to the Bioconductor Workshop website.