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/...]

Other methods (not recommended)

Flair consists of six modules. The first three are align, correct, and collapse. They are the most used, so we will refer to them here as basic Flair.

The other three modules are quantify, flair_diffExp, and flair_diffSplice. Together with basic Flair these are called full Flair. These three additional modules have more dependencies than basic Flair so if you don’t need them, you will not need the modules listed under 5.

There are other ways to install Flair:

• pip install flair-brookslab will install basic Flair and all necessary python modules (see below)

• Download the latest release

• Use git to check out the current flair repository

Requirements

1. Bedtools

2. samtools

3. minimap2

If you do not use pip install or conda env create`, you will also need:

4. python v3.6+ and python modules:

   • numpy=1.9.*

   • tqdm

   • ncls

   • pybedtools

   • mappy

   • pysam=v0.8.4+

5. full Flair additional python modules:

• Cython

• pandas

• rpy2=2.9.*

• R

• r-ggplot2=2.2.1

• r-qqman

• bioconductor-deseq2

• bioconductor-drimseq

• bioconductor-stager

• matplotlib

• seaborn

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_basic_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.