X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=README;h=5735c8e5acab9d694c3ab25aa3ab2827dffa1b47;hp=10f032b165c265318f2f08382caa5cdce4e22fa2;hb=a92455a4db78cdc97d94f7bddb1929096abab1f2;hpb=df05b75cc541ddf6a0a6fa62e50bbff53df03e30

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-Jalview Readme
---------------
+Jalview README
+==============
 
+Welcome !  
 
-The source is available as a tar file and comes complete with the GNU General Public License. 
+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.
 
-To build the application you will need a J2SDK 1.6+. 
+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.
 
-An Ant build file (build.xml) is provided, you will need to install Apache Ant first. 
-Run ant to view usage which will display a list of useful build targets.
+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.
 
-Jalview is primarily developed with eclipse, and a .project file is provided to simplify importing the source into your own eclipse workspace. A NetBeans nbbuild.xml file is also provided for developing Jalview with NetBeans - but this is not officially supported.
+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:
 
-You may also be able to use Borland JBuilder to build Jalview. A JBuilder project file 
-(JalviewX.jpx, JalviewApplet.jpx) for both application and applet is provided, 
-but the library dependencies are almost certainly out of date. See the build.xml 
-for current dependencies.
+gradle test # run functional test suite
 
-For more help, read the file doc/building.html
+gradle shadowJar # build a single executable Jar under build/libs/
 
+gradle jalviewjs # builds JalviewJS under build/jalviewjs  
 
-##################
-
-To run application:
-
-java -Djava.ext.dirs=JALVIEW_HOME/lib -cp JALVIEW_HOME/jalview.jar jalview.bin.Jalview
-
-Replace JALVIEW_HOME with the full path to Jalview Installation Directory.
-
-##################
-
-
-If you use a proxy server add 
-
--Dhttp.proxyServer=YOUR.SERVER -Dhttp.proxyPort=YOURPORT
-
-If the proxy server requires authentication, add
-
--Dhttp.proxyUser=USERNAME -Dhttp.proxyPassword=PASSWORD
+If you want to build JalviewJS then you will also need to download
+Eclipse for your platform, since transpilation requires an Eclipse
+plugin.