<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
+ 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
+ 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
+ <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
+ 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>
git://source.jalview.org / jalview.git / blobdiff