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 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.
--
- - + + +
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 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.
++
+ +