-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 1.7+.
+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-but the library dependencies are almost certainly out of date.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...
-[ NOTE: when using the -classpath option with the '*' wildcard, the argument must be quoted to avoid shell expansion of the wildcard,
- ALSO, the wildcard MUST be as DIR/* and not DIR/*.jar etc or it will not be interpreted correctly ]
-
-on Windows use:
- java -classpath "JALVIEW_HOME/lib/*;JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
-and on MacOS or Linux:
- java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
-
-Replace JALVIEW_HOME with the full path to Jalview Installation Directory. If building from source:
-
- java -classpath "JALVIEW_BUILD/dist/*" jalview.bin.Jalview
-
-
-##################
-
-
-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.
git://source.jalview.org / jalview.git / blobdiff