ArchR_Website

To build the website:

1. Make sure you have the most up-to-date version of the DESCRIPTION file and the .Rd files created from ArchR when the package is built. The DESCRIPTION file should be copied into the main folder of this repository. The .Rd files contain the function documentation and should be copied into /man/.
2. In the DESCRIPTION file, add the following tag "URL: https://www.ArchRProject.com"
3. You must have pandoc installed.
4. You must have the pkgdown R library installed.
5. In R, from the main repository directory (containing the index.md file), run build_site(). This will create a lot of HTML files in the /docs/ folder.

To build the book:

1. Make sure the following packages are installed:

pdftools

2. Clone this ArchR_Website repository and navigate to the /bookdown/ folder.
3. Delete the HTML files in the /docs/bookdown folder
4. Launch R
5. Load the renv environment and the bookdown package:

   library(renv)
   renv::restore(lockfile="/path/to/lockfile")
   #follow instructions to activate and load libraries
   library(ArchR)
   library(bookdown)
   

6. Run bookdown::render_book(input = "index.Rmd", output_dir = "../docs/bookdown") from the /bookdown/ directory where index.Rmd is located.

Once you've built the book, copy all of the HTML files and required figures etc. into the /docs/bookdown/ folder

Notes on bookdown installation and building

1. Because the v1.0.1 ArchR renv lockfile (as of 1/11/22) uses xfun v0.28, I had to manually install the tinytex v0.35 prior to installing bookdown using

devtools::install_version("tinytex", version = "0.35", repos = "http://cran.us.r-project.org")

2. It seems like the building of the book struggles when packages need to be installed on the fly. This for example caused problems in the drosophila genome building section where bookdown just stalls

3. I am having trouble with conflicts between the renv packages and my locally installed packages?

4. library(parallel) causing problems in ArchR v1.0.1

5. Had to install a few packages - svglite