From b46d5c20908ebf8ca44175a873e26611c7573adb Mon Sep 17 00:00:00 2001 From: Alexandru Mahmoud Date: Thu, 5 Oct 2023 11:58:44 -0400 Subject: [PATCH] Add README --- README.md | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..2b3a803 --- /dev/null +++ b/README.md @@ -0,0 +1,35 @@ +## Bioc2u (alpha): Ubuntu Binaries for Bioconductor packages + +This project aims to extend [r2u](https://github.com/eddelbuettel/r2u), +in hopes of providing a repository of Ubuntu binaries via `apt` for all Bioconductor packages. + +**Bioc2u is current only available for Ubuntu Jammy and is still in alpha development.** + +### Getting started + +If you wish to get started in a minimal environment, a relatively small docker container is provided, built on `ubuntu:jammy`, and providing the initial `apt` +and `R` setup to get you started. You may use this container via `docker run --rm -it ghcr.io/bioconductor/bioc2u-user:jammy`. Alternatively, if you are on +an Ubuntu machine, you may set up the `bioc2u` and `r2u` repositories for your local system's `apt` by using the provided script! + +In an Ubuntu environment (tested in `ubuntu:jammy` container), you may use the [`apt_setup.sh`](https://github.com/Bioconductor/bioc2u/blob/devel/apt_setup.sh) +script which will set up the Bioc2u `apt` repository and install R, and basic packages such as BiocManager. +```bash +# Install curl if missing +apt update -qq +apt install -y --no-install-recommends curl ca-certificates +# Run apt script +curl https://raw.githubusercontent.com/Bioconductor/bioc2u/devel/apt_setup.sh | sudo bash +``` +After the initial setup, you may use `apt` or `install.packages()` freely. Installing packages through `apt` can be done in any shell session, by using the +`r-bioc-` prefix and the all-lowercase name of the package, eg `apt install -y r-bioc-biocmanager`. You may alternatively continue to use R traditionally. + +By default, the `r-core-base` installation (provided by the r2u project), uses the [`bspm`](https://cran.r-project.org/web/packages/bspm/index.html) package to enable the usage of the package manager +when installing packages from within R via `install.packages()` or `BiocManager::install()`. You may thus continue to use R as you would outside of this +environment, and observe the speedup resulting from R using the `apt` package manager under the hood. + +### Status / TODOs (alpha) +- 1800+ packages built for ubuntu jammy + - TODO: Build for ubuntu focal + - TODO: Collect failure logs, then address common errors and missing build-dependencies +- Repository public without signed key (TODO: gpg key and update repository) +- Repository hosted on JS2 (TODO: host on OSN)