X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fcommandline.html;h=9cffc515bc171e1bffb75af7676e1645641b859c;hb=0b8133635dc649fb7710b9390a718c8f27a7f276;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/features/commandline.html b/help/html/features/commandline.html index e18e273..9cffc51 100644 --- a/help/html/features/commandline.html +++ b/help/html/features/commandline.html @@ -1,18 +1,65 @@ + * 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. +

+

 

+

 

+ +