Running Jalview from the command line

Jalview is most easily run from the command line if you have built it from source, or via the 'Jalview' executable created from the InstallAnywhere Jalview installation. Both of these mechanisms allow true command line execution of Jalview - allowing you to provide additional options.

The Java Webstart version of Jalview can be executed from the command line using something like : 

javaws https://www.jalview.org/webstart/jalview.jnlp -open
 yourFileName
But, this is not guaranteed to work on all versions of webstart on all operating systems, and doesn't let you execute Jalview with any additional parameters.

Running Jalview from the InstallAnywhere installation

If you install with InstallAnywhere you can use several more commands. However, if you call the application with the link provided by InstallAnywhere any output from the application will be sent to output.txt, not standard out.
The Jalview application also requires a number of additional libraries on the class path. The command line below adds the Jalview installation's 'lib' directory to the list of directories that are searched for jars to be added to the classpath: 

java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE]

Use '-help' to get more information on the command line arguments that Jalview accepts.