X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=README;h=5735c8e5acab9d694c3ab25aa3ab2827dffa1b47;hp=e8c44a99d89d1464bb56163c4cc565ac51feb064;hb=fc77dfd068b74f1ba81927c098b97667eb01e255;hpb=fab0afc9e1e7a5ca460f0cbd48545536f989a435 diff --git a/README b/README old mode 100755 new mode 100644 index e8c44a9..5735c8e --- a/README +++ b/README @@ -1,72 +1,34 @@ -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JalviewApplet.jpx) for both application and applet is provided, -but the library dependencies are almost certainly out of date.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 -## +gradle shadowJar # build a single executable Jar under build/libs/ -Jalview-JS +gradle jalviewjs # builds JalviewJS under build/jalviewjs -To enable transpilation of Jalview's code: - -1. Locate the 'dropins' directory in your eclipse installation and copy swingjs/net.sf.j2s.core.jar to it. - - typically it is at the top of the Eclipse installation, or on OSX under Eclipse.app/Contents/Eclipse - -2. Restart Eclipse - -3. If all is well you should see the 'Java2Script' builder is listed as the primary builder for the Jalview project. - if not, this is because your properties file needs to have the standard java builder replaced with the following: - net.sf.j2s.core.java2scriptbuilder - -- otherwise Javascript files will now be generated in the site/swingjs/j2s directory whenever a build occurs - -4. Execute the 'unzip-to-site' task (if it isn't automatically run) to update the site directory with the latest versions of SwingJS, varna-js, JSmol and other dependencies required by Jalview. - - - - - -## - -For more help, read the file doc/building.html - - -################## - -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.