In Bioconductor/workshopbuilder: This package compiles workshops from different locations into a central bookdown workshop repository

knitr::opts_chunk$set(echo = TRUE, eval = FALSE)

Installation

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

BiocManager::install("Bioconductor/workshopbuilder")

.options <- workshopbuilder:::.options

Set up

workshopbuilder ships with a number of package options to make management of workshop directories and repositories easier. The three main options are:

1) Workshop book repository location on GitHub

.options$set("BOOK_REPO", "Bioconductor/BiocWorkshops2019")

2) Local workshop book directory

.options$set("LOCAL_REPO", normalizePath("~/BiocWorkshops2019"))

3) Local workshop repositories directory

.options$set("REPOS_PATH", normalizePath("~/Bioconductor/Workshops"))

Workflow Overview

The workshopbuilder package facilitates the installation and rendering of the workshop book repository along with all the component repositories.

The individual workshop repositories are documented as GitHub issues in the main workshop book repository.

We then take the workshops and the main book repository and clone them all. We install and transfer vignettes to the main book repository and run a render step to generate the book document.

Read the issues from the repository issues comments

workshopbuilder takes issues with a [Workshop] tag and pulls workshops from the URL provided in the body of the issue.

Clone the workshop repositories (pull if already available)

The package uses git2r to clone all invididual workshop repositories (or those otherwise indicated) to the location as specified by the REPOS_PATH package option (see setup).

Install the workshops

library(workshopbuilder)

shopstatus <- installWorkshops("MultiAssayWorkshop",
    exclude = FALSE, ncpus = 12)

Run R CMD INSTALL * on each repository

The output of the installation can be seen by using getStatus:

getStatus()

(optional) Post repository installation status

The text of the installation output can be posted as a comment in the issue by running postStatus.

Note. This requires a GITHUB_PAT Personal Authentication Token (PAT) environment variable (usually in .Renviron).

postStatus()

Inspect the data.frame with metadata for each workshop repository

This data.frame includes metadata including the issue number and URL location

shopstatus

Capture the output of the installation and save to a file

Installation output is saved to a file in the REPOS_PATH folder; defaults to "buildout".

list.files(
    file.path(.options$get("REPOS_PATH"), "buildout")
)

Clone the main workshop book repository

This can be done by running the getBookRepo function. It will take the BOOK_REPO package value and clone from GitHub.

getBookRepo()

Add workshops to the DESCRIPTION file

Using the desc package, we then add all the successfully installed workshops to the DESCRIPTION file of the book repository.

Notice that shopstatus has a logical column that indicates a successful installation called 'install'.

addWorkshops(shopstatus)

Transfer vignettes to the main workshop book repository

We then transfer all successful workshop Rmd files to the main book repository for building.

rmds <- transferVignettes(shopstatus)

Include the Rmd files in the configuration file for book building

We make sure to document the added R Markdown files in the _bookdown.yml configuration file.

addRmdFiles(rmds)

Render the book

The configuration files that are pre-included in the workshop book repository allow the book to build. In the future, we may consider adding this step via the R interface. We use these files to render the book into the different formats depending on the input to the renderWorkshops format.

renderWorkshops(format = "all")

repo)

Bioconductor/workshopbuilder documentation built on Dec. 2, 2019, 11:41 p.m.