Installing bngal
Command-line utility (bngal-cli)
R package only with CRAN

Installing `bngal`

Although bngal is released as a standalone R package and can be interactively used in an IDE such as RStudio, I strongly recommend running the command-line utility wrapper (bngal-cli) to simplify its use, especially for first-time users. bngal-cli is currently only tested on MacOS and Linux.

You can quickly install both the bngal R package and its command-line utility wrapper via the following instructions:

Command line utility (recommended)

There are two ways to install the command line utility: DockerHub or Singularity. I recommend using one of the images hosted on DockerHub (do note your chip architecture - discussed further below). An installation route is also available from Anaconda or CRAN.

Docker (and Singularity)

Before pulling from DockerHub, please note your chip architecture - arm64 (e.g., Apple Silicon) or amd64 / x86_64 (e.g., Intel). You will want to pull the right image matched to your chip type. The bngal images are bootstrapped with micromamba-docker:

Image Tag	Version	Architecture
`mjsel/bngal:1.0.1`	`1.0.1`	`amd64 / x86_64`
`mjsel/bngal:1.0.1-arm64`	`1.0.1`	`arm64`
`mjsel/bngal:1.0.0`	`1.0.0`	`amd64 / x86_64`
`mjsel/bngal:1.0.0-arm64`	`1.0.0`	`arm64`

bngal-cli is easily installable if you use Docker. You will only need to install one of these, depending on your architecture:

docker pull mjsel/bngal:1.0.1
docker pull mjsel/bngal:1.0.1-arm64 

Alternatively, you can pull the same image if you use Singularity:

singularity pull docker://mjsel/bngal:1.0.1
singularity pull docker://mjsel/bngal:1.0.1-arm64

Anaconda virtual environment

If you instead prefer to use conda, please follow the instructions as follows.

Install the appropriate Anaconda version for your operating system if you don’t have it already.
Clone the bngal-cli GitHub repository into your directory of choice (my-directory) and run the setup script in a bash or zsh shell session. This will install the bngal R package within a new conda environment called “bngal”:

cd my-directory
git clone https://github.com/mselensky/bngal-cli --branch v.1.0
cd bngal-cli
bash bngal-setup.sh

And that’s it! Sit tight and grab a coffee while bngal-cli installs. It may take a few minutes.

Once you successfully install and activate the bngal environment, you can remove the bngal-cli folder. When the bngal environment is active, you will have access to two bngal-cli functions:

`bngal-cli` functions

Function	Application
`bngal-build-nets`	Build network model(s) according to defined cutoffs
`bngal-summarize-nets`	Summarize and visualize network statistics from `bngal-build-nets`

R package only with CRAN

If you only want to use the bngal R package interactively, you can install it and its dependencies within an active R session via:

source("https://raw.githubusercontent.com/mselensky/bngal-cli/main/R/install-R-pkgs.R")

Please refer to the internal documentation when using the standalone R package.

Table of contents

Installing bngal