<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * 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>
+ -->
+<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>
+ <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