Jalview README
==============

Welcome !  

Jalview is free (GPLv3 licensed) software for creation, interactive
visualisation and analysis of alignments of biological sequences. It
was developed by Michele Clamp in 1996, and now maintained by the
Jalview Development team in the Barton group at the University of
Dundee.

If you'd like to help out please check out the website
(www.jalview.org) and get in touch. See CITATION for the canonical
reference if you need to cite Jalview.

To build the Jalview Desktop application and JalviewJS, the JavaScript
transpiled version (with the help of java2script, courtesy of Bob
Hanson), you will need a Java 11 JDK and a recent version of
Gradle. For development we recommend Eclipse - you should be able to
import Jalview as a Gradle project with the Buildship plugin.

Most likely you'll want to take a look at doc/building.md to find out
exactly what is needed. If you already have Java 11 and Gradle, then
the tldr:

gradle test # run functional test suite

gradle shadowJar # build a single executable Jar under build/libs/

gradle jalviewjs # builds JalviewJS under build/jalviewjs  

If you want to build JalviewJS then you will also need to download
Eclipse for your platform, since transpilation requires an Eclipse
plugin.
