* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
---!>
-<head><title>Running Jalview from the command line</title></head>
-<body>
- <p><strong>Running Jalview from the command line</strong></p>
- <p>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.</p><p>
-The Java Webstart version of
- jalview can be executed from the command line using something like
- :
- <pre>javaws http://www.jalview.org/webstart/jalview.jnlp -open
- <em>yourFileName</em></pre>
- 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.
- <p><strong>Running jalview from the InstallAnywhere
- installation</strong></p>
- <p>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.<br>
- 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:</p>
-<pre>java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE] </pre>
- <p>Use '-help' to get more information on the <a
- href="clarguments.html">command line arguments</a> that Jalview
- accepts.</p>
- <p> </p>
- <p> </p>
- </body>
- </html>
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