X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fcommandline.html;h=e393701da83b50702bf18a34280e15ccdb54c63a;hb=43d326c3a7616aedecfce6f7980b3831ec25243a;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/features/commandline.html b/help/html/features/commandline.html index e18e273..e393701 100644 --- a/help/html/features/commandline.html +++ b/help/html/features/commandline.html @@ -1,18 +1,55 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> +Running Jalview from the command line + +

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.

+

 

+

 

+ +