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--- setup:installation [2020/06/04 18:20] – [Video demonstration] pseudomoaner
+++ setup:installation [2022/11/15 11:24] (current) – pseudomoaner
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 === Step 1: Downloading the source code ===
-To download the latest version of FAST, please click [[https://mackdurham.group.shef.ac.uk/FAST_v0_9_1.zip|here.]] You should now extract the zipped FAST folder you just downloaded to a known location. The resulting directory is referred to as your FAST code directory.
+To download the latest version of FAST, please click [[https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/FASTdownloads/FAST_v2_1.zip|here.]] You should now extract the zipped FAST folder you just downloaded to a known location. The resulting directory is referred to as your FAST code directory.
 The latest release of FAST's source code is also available at [[https://github.com/Pseudomoaner/FAST|Github]]. Please note however that this version does not contain the full version of Bio-Formats, and as such cannot be used to import datasets.
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 into your command line after you have temporarily added it to your path as describe above.
+=== Step 3: Adding toolboxes to Matlab ===
+FAST currently relies, in part, on functions available in several toolboxes. If you do not already have these installed, you can find guidance on how to install them [[https://uk.mathworks.com/help/matlab/matlab_env/get-add-ons.html|here]].
+Toolboxes FAST requires to run:
+  * Image processing toolbox
+  * Signal processing toolbox
+  * Statistics and machine learning toolbox
+Work to remove these dependencies is currently underway, and should be completed in a future release. If you do not have access to licenses for these toolboxes, currently you will need to use the stand-alone version of FAST (see below).
 ===== Option 2: Installing the stand-alone version =====
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 Please note that if you choose this option, FAST's output will need to be converted from .mat files to structures appropriate for the platform of your choice. Functions for performing this conversion can be found in the [[post:post-processing_toolbox#track_format_conversion|post-processing toolbox]].
+==== Platform specific instructions ====
+=== MacOS ===
+When trying to start the installation process, MacOS will warn you that the app was developed by an unidentified developer and block its installation. To override this, please follow the instructions provided here:
+https://support.apple.com/en-gb/guide/mac-help/mh40616/mac
+=== Linux ===
+Once you have completed the installation process, you will have generated two new folders, one corresponding to your installation of FAST (the location of which will be denoted as \Path\To\FAST\) and one to your installation of the Matlab runtime (\Path\To\Matlab_runtime\). To run FAST, simply type the following into the terminal:
+<code>
+\Path\To\FAST\application\run_FAST.sh \Path\To\Matlab_runtime\vXX\
+</code>
+where vXX denotes the version of the Matlab runtime installed in your runtime directory (e.g. 'v95').
+==== List of FAST features not compatible with stand-alone versions ====
+Unfortunately, not all parts of FAST are currently supported in the stand-alone versions of the software. To make use of these capabilities, you will instead need to use FAST directly in Matlab (option 1):
+  * [[usage:advanced_usage#custom_feature_extraction|Custom feature extraction]]
+  * [[usage:batch_processing|Batch processing]]
+  * [[usage:advanced_usage#informing_the_division_detection_module|Division detection customization]]
 ===== Video demonstration =====
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