X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fcommandline.html;h=9cffc515bc171e1bffb75af7676e1645641b859c;hb=74f810edbb5063639a53e4f34f7bb8e74235c4ef;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
+ 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. +
++
+ +