Quick start
===========

This page provides instruction for installing RAFT and running a demonstration workflow in a local environment.

.. note::

   Before you begin, make sure the following are installed on your system:

   - **Python 3.9+**
   - **Nextflow**
   - **Singularity or Apptainer**

   If any of these are missing, install them before running ``raft setup``.
   See :doc:`running-raft-locally` for more details.

Install RAFT
------------

Users can install RAFT using

.. code-block:: console

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


Initialize a RAFT workspace
---------------------------

RAFT can be initialized in the current directory using:

.. code-block:: console

  $ raft setup --default

Run a demonstration workflow
----------------------------

Run a demo workflow:

.. code-block:: console

  $ raft run-demo --workflow lens --version v1.9-dev

View example report
--------------------

An example of a report can be viewed using:

.. code-block:: console

  $ raft generate-reports --demo

.. note::

   A hosted example report using synthetic data is available `here <https://spvensko.github.io/raft-ui/raft-viewer.html?demo=1>`_.


Run on your own data
--------------------

Once you're ready:

- See :doc:`choosing-your-environment` to decide between local and cloud execution.
- See :doc:`workflows` to find the right workflow for your data.
- See :doc:`datasets` for how to prepare your samples
- See either :doc:`running-raft-locally` or :doc:`running-raft-on-the-cloud` for a full overview of the run process.
- See :doc:`accessing-and-reviewing-outputs` for how to access outputs and review results