Saite delivered as self installing / running uberjar
wget http://bioinformatics.bc.edu/~jsa/aerial.aerosaite-1.4.4-standalone.jar
if the above is not working use the following mirror (as of 21-Feb-2023 the bioinformatics.bc.edu site is undergoing a maintenance migration and will be unavailable to the public for some time)
wget -O aerial.aerosaite-1.4.4-standalone.jar "https://drive.google.com/uc?id=1b8SjAKFqP8u7BS3D3XxgqEQCOnN1_1KZ"
Or use curl or whatever else you like for fetching web located resources
Now able to use JDK 8 or JDK 11+. However, only tested with 8 and 11, while 16 is deprecated with binary incompatibilities with 17. In general just stick with LTS versions. UPDATE jdk-17 has been tested and it also works!
java -jar aerial.aerosaite-1.4.4-standalone.jar --install
take the defaults, in particular ~/.saite for application home directory. MKL suitable for Neanderthal will be downloaded as part of the installation. It will also set up the paths on Linux and MacOS. Windows will get the libraries in the .saite/Libs directory, but auto setup is not yet available for Win as I haven't had access to be able to put together a working script for it.
If you already have Saite, you can update it to the latest version with the --update switch.
java -jar aerial.aerosaite-1.4.4-standalone.jar --update
To run, the simplest and best way is to use the scripts available in the .saite home directory:
linux-runserver: Linux JVM 8jvm11+-linux-runserver: Linux JVM 11+mac-runserver: MacOS JVM 8jvm11+-mac-runserver: MacOS JVM 11+win-runserver.bat: Windows 10 JVM 8jvm11+-win-runserver.bat: Windows 10 JVM 11+
As of 1.4.4 there are now 'base' scripts for Windows 10. They do not include code able to setup the MKL libraries. The reason for separate JVM 8 and 11+ versions is that JVM 9+ requires added switches to support Neanderthal and DeepDiamond.
For Windows, there has been some limited testing of the scripts and they should work. But if not, and you are Windows user, you should be able to figure out the run command based on what you can see in the scripts. Or better yet, if you really know how to do this, a PR would be great!!
Once up and running navigate to localhost:3000 (unless you changed the port in your scripts/run command). You will see this as the startup 'page/screen':
Click on the Upload Document button 
. Then select Scicloj from Session and then select SaiteOverview. After a couple seconds or so, you should see this page. You are placed in the gallery tab, but go to the left and start with Overview and just go left to right for a general overview.
