.. _installing-label:

Installing Flair
================

BioConda Install
~~~~~~~~~~~~~~~~

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

.. code:: sh

   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:

.. code:: sh

   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: 

.. code:: sh

   conda env update --name flair --file https://github.com/BrooksLabUCSC/flair/releases/download/v2.2.0/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:

.. code:: sh

   conda env create -n flair -c conda-forge --file https://github.com/BrooksLabUCSC/flair/releases/download/v2.2.0/flair_conda_env.yaml
   conda activate flair
   
To add the `diffexp` or `diffsplice` dependencies:

.. code:: sh

   conda env update --name flair --file https://github.com/BrooksLabUCSC/flair/releases/download/v2.2.0/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:

.. code:: sh

    docker pull brookslab/flair:2.2.0
    docker run -v [your_path_to_data]:/data brookslab/flair:2.2.0 flair [align/correct/...]

.. _pip-install-label:

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 <https://github.com/arq5x/bedtools2/>`_
- `samtools <https://github.com/samtools/samtools/releases>`_
- `minimap2 <https://github.com/lh3/minimap2>`_

.. code:: sh

   pip install flair-brookslab


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

- `DESeq2 <https://bioconductor.org/packages/release/bioc/html/DESeq2.html>`__
- `ggplot2 <https://ggplot2.tidyverse.org>`__
- `qqman <https://cran.r-project.org/web/packages/qqman/index.html>`__
- `DRIMSeq <http://bioconductor.org/packages/release/bioc/html/DRIMSeq.html>`__
- `stageR <http://bioconductor.org/packages/release/bioc/html/stageR.html>`__

.. code:: sh

   pip install flair-brookslab[diffexp]


Running from GitHub clone
~~~~~~~~~~~~~~~~~~~~~~~~~

The dependence must first be installed as for :ref:`pip-install-label`.

.. code:: sh

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