Installing Flair

BioConda Install

The easiest way to install Flair and all of its dependencies is via BioConda:

conda create -n flair -c conda-forge -c bioconda flair
conda activate flair
flair [align/correct/...]

On Apple Silicon Mac systems (ARM64 CPUs: M1, M2, …) you must use:

CONDA_SUBDIR=osx-64 conda create -n flair
conda activate flair
conda config --env --set subdir osx-64
conda config --add channels bioconda
conda config --add channels conda-forge
conda install flair

Note that mamba currently fails to install FLAIR on Mac ARM64.

If you are going to use the diffexp or diffsplice modules, you need to add addition packages to the Conda environment with:

conda env update --name flair --file https://github.com/BrooksLabUCSC/flair/releases/download/v3.0.0b1/flair_diffexp_conda_env.yaml

Conda Install from GitHub Release

BioConda release are often delayed by the manual review process. To create a Conda environment from a release in GitHub, use:

conda env create -n flair --file https://github.com/BrooksLabUCSC/flair/releases/download/v3.0.0b1/flair_conda_env.yaml
conda activate flair

To add the diffexp or diffsplice dependencies:

conda env update --name flair --file https://github.com/BrooksLabUCSC/flair/releases/download/v3.0.0b1/flair_diffexp_conda_env.yaml

Running FLAIR with Docker

FLAIR releases are also available as a Docker images, which includes the R dependencies to run diffexp and diffsplice. Obtain and run the FLAIR Docker with:

docker pull brookslab/flair:3.0.0b1
docker run -v [your_path_to_data]:/data brookslab/flair:3.0.0b1 flair [align/correct/...]

Pip install

To install with pip, you must first install these packages. This can be done with Conda, yes system package manager or by downloading and compiling,

• bedtools

• samtools

• minimap2

pip install flair-brookslab

or to install the current code from github:

pip install git+https://github.com/BrooksLabUCSC/flair.git

If you already have FLAIR install, you will need to uninstall it first to update the code, since the version number will not have changed in the tree.

pip uninstall flair-brookslab
pip install git+https://github.com/BrooksLabUCSC/flair.git

The``flair diffexp`` and flair diffsplice modules require R , along with these R packages. Some of these do not work on Apple Silicon.

• DESeq2

• ggplot2

• qqman

• DRIMSeq

• stageR

Running from GitHub clone

The dependence must first be installed as for Pip install.

git clone https://github.com/BrooksLabUCSC/flair.git
cd flair
./bin/flair [align/correct/...]