<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* 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/>.
--->
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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>
git://source.jalview.org / jalview.git / blobdiff