Installing RAFT
===============

RAFT is the Nextflow-based workflow manager used to run the LENS workflow.

Users should refer to useraft.io for the latest information, but we have
provided a brief overview for install RAFT below.

Installing through Conda
________________________

Users should ensure Conda is installed prior to install RAFT. Users can find
installation instructions on the `Conda documentation page
<https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html>`_.

To install RAFT using Conda, run:

.. code-block:: console

  $ conda install -c bioconda -c conda-forge -c raft reproducible-analyses-framework-and-tools

Installing through pip
______________________

Installing RAFT through ``pip`` will require users to separately install `Apptainer <https://apptainer.org/docs/admin/main/installation.html>`_ and `Git <https://git-scm.com/book/en/v2/Getting-Started-Installing-Git>`_.

To install RAFT using pip, run:

.. code-block:: console

  $ pip install --user reproducible-analyses-framework-and-tools

.. note::
  ``pip`` will install ``raft`` to ``~/.local/bin``.
  Please ensure this directory is in your ``$PATH`` 
  (``export PATH=$PATH:~/.local/bin``).

Setup
_____

RAFT requires a directory consisting of various folders including:
``/Projects``, ``/References``, and ``/Metadata``. This directory will also
contain the RAFT configuration file.

To set up RAFT, run:

.. code-block:: console

  $ raft.py setup

Users will be prompted to provide paths for each required subdirectory (with
sensible defaults). 

A default installation (in which all subdirectories are created in the user's
current working directory) can be created by running the following command in
the terminal:

.. code-block:: console

  $ raft.py setup --default

.. note::
   Users installing with the ``--default`` option should ensure their working
   directory does not have unreasonable (e.g. <1 TB) storage limitations.


At this point, RAFT is installed and users are ready to run the LENS workflow.