X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fcommandline.html;h=f99e20c7ebc3fc6acba7669def44758bfb4ac91a;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/features/commandline.html b/help/html/features/commandline.html index e18e273..f99e20c 100644 --- a/help/html/features/commandline.html +++ b/help/html/features/commandline.html @@ -1,6 +1,6 @@ +
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.
++
+ +