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Installing FaST
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System requirements
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FaST requires at least 32 Gb of RAM and a multicore processor with at least 8 cores/16 threads.
More threads may marginally speed up the analysis, especially if using a SSD drive.
All the currently available public datasets compatible with FaST can be analysed with 32 Gb of RAM.


Software requirements
-------------------

FaST has been developed to run in a bash shell on Linux OS.
FaST currently requires:

* bedtools v2.30.0 or later.
* samtools v1.19.2 (but any version will likely work as the only samtool invoked by FaST is "samtools view").
* STAR v2.7.11a or later.
* spateo-release v1.0.2 (for RNA segmentation only).
* scanpy v1.10.1 or later.

It is advisable to take advantage of the `FaST_env.yml <https://github.com/flcvlr/FaST/blob/main/data/FaST_env.yml>`_ 
file in the data folder to create a dedicated environment.


Installation
-------------------

Fast comes as a set of bash, Perl and Python scripts. To install it you should simply clone the github repository
to a suitable location of your filesystem, using the command:

.. code-block:: bash

    $ git clone https://github.com/flcvlr/FaST /path/to/FaST

Optionally, you can add the /path/to/FaST/scripts/ directory to your PATH evironmental variable. This will allow you to run FaST by just typing:

.. code-block:: bash
  
    $ FaST -h

instead of:

.. code-block:: bash
  
    $ /path/to/FaST/scripts/FaST -h


If you choose to run FaST in the dedicated environment, remember activating the environment before running FaST.