+ 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 http://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 all the jar files in the
+ Jalview installation's 'lib' directory to the classpath, as well as
+ the Jalview application jar file:
+
java -classpath "$INSTALL_DIR$/lib/*:$INSTALL_DIR$/jalview.jar" jalview.bin.Jalview -open [FILE]+
+ Use '-help' to get more information on the command line arguments that + Jalview accepts. +
++
+ +