To enable transpilation of Jalview's code:
-1. Locate the 'dropin' directory in your eclipse installation and copy swingjs/net.sf.j2s.core.jar to it.
+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:
<name>net.sf.j2s.core.java2scriptbuilder</name>
- 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.
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-To run application:
+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 ]
-java -Djava.ext.dirs=JALVIEW_HOME/lib -cp JALVIEW_HOME/jalview.jar jalview.bin.Jalview
+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 -Djava.ext.dirs=JALVIEW_BUILD/dist -cp JALVIEW_BUILD/dist/jalview.jar jalview.bin.Jalview
+ java -classpath "JALVIEW_BUILD/dist/*" jalview.bin.Jalview
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git://source.jalview.org / jalview.git / blobdiff