3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
4 * Copyright (C) 2014 The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
20 <head><title>Running Jalview from the command line</title></head>
22 <p><strong>Running Jalview from the command line</strong></p>
23 <p>Jalview is most easily run from the command line if you have built
24 it from source, or via the 'Jalview' executable created from the
25 InstallAnywhere jalview installation. Both of these mechanisms allow
26 true command line execution of jalview - allowing you to provide
27 additional options.</p><p>
28 The Java Webstart version of
29 jalview can be executed from the command line using something like
31 <pre>javaws http://www.jalview.org/webstart/jalview.jnlp -open
32 <em>yourFileName</em></pre>
33 But, this is not guaranteed to work on all versions of webstart on all
34 operating systems, and doesn't let you execute Jalview with any
35 additional parameters.
36 <p><strong>Running jalview from the InstallAnywhere
37 installation</strong></p>
38 <p>If you install with InstallAnywhere you can use several more commands.
39 However, if you call the application with the link provided by InstallAnywhere
40 any output from the application will be sent to output.txt, not standard
42 The jalview application also requires a number of additional
43 libraries on the class path. The command line below adds the Jalview
44 installation's 'lib' directory to the list of directories that are
45 searched for jars to be added to the classpath:</p>
46 <pre>java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE] </pre>
47 <p>Use '-help' to get more information on the <a
48 href="clarguments.html">command line arguments</a> that Jalview