Other environments

The easiest way to install FLAIR and all of its dependencies is via conda:

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

It is also possible to get the full FLAIR setup as a docker image:

docker pull brookslab/flair:latest
docker run -w /usr/data -v [your_path_to_data]:/usr/data brookslab/flair:latest flair [align/correct/...]

You can build a Conda environment from GitHub, for example for release v2.1.0:

conda env create -n flair -f https://raw.githubusercontent.com/BrooksLabUCSC/flair/refs/tags/v2.1.0/misc/flair_conda_env.yaml
conda activate flair

You can also build a Conda environment from the source tree with .. code:: sh

git clone git@github.com:BrooksLabUCSC/flair.git cd flair git checkout v<version-tag> conda env create -n flair -f misc/flair_conda_env.yaml conda activate flair pip install .

Manual installation methods

Requires not installable with pip

  1. Bedtools

  2. samtools

  3. minimap2

Pip install

pip install flair-brookslab will put the latest FLAIR release in your $PATH, as well as the helper scripts discussed in this manual. It also installs all python modules needed to run basic FLAIR. If you want to use full FLAIR, install the packages listed under point 5 in the list above.

Download the latest release

Navigate to the FLAIR release page and select one of the source code files under Assets. Exctract the file and navigate to the resulting flair directory. Add FLAIR and the helper scripts to your $PATH for instance (in Linux) with export PATH=$(pwd)/bin:$PATH.

Make sure to (pip) install the python modules listed above. If you have conda, you can create a basic FLAIR environment using

conda env create -f misc/flair_conda_env.yaml

Download the latest code

Check out the current FLAIR repository from github. Please be aware that while this may have the latest bug fixes, it’s quite possible that new bugs were introduced. This method is only useful if you have reported a problem and a FLAIR developer lets you know it has been fixed.

Once you have cloned the repository, navigate to the /flair directory. Follow the steps as described under Download the latest release.

flair_diffExp and flair_diffSplice

Two other programs are available in the source tree, although they now deprecated: flair_diffExp, and flair_diffSplice. The dependencies are not include in the standard conda or pip installs. The following packages are required

  • Cython

  • pandas

  • rpy2=2.9.*

  • R

  • r-ggplot2=2.2.1

  • r-qqman

  • bioconductor-deseq2

  • bioconductor-drimseq

  • bioconductor-stager

  • matplotlib

  • seaborn

These maybe added to standard conda environment with:

` conda env update --name flair --file misc/flair_diffexp_conda_env.yaml pip install -e .[diffexp] `