-<html>\r
-<head><title>Running Jalview from the command line</title></head>\r
-<body>\r
- <p><strong>Running Jalview from the command line</strong></p>\r
- <p>Jalview is most easily run from the command line if you have built\r
- it from source, or via the 'Jalview' executable created from the\r
- InstallAnywhere jalview installation. Both of these mechanisms allow\r
- true command line execution of jalview - allowing you to provide\r
- additional options.</p><p>\r
-The Java Webstart version of\r
- jalview can be executed from the command line using something like\r
- :\r
- <pre>javaws http://www.jalview.org/webstart/jalview.jnlp -open\r
- <em>yourFileName</em></pre>\r
- But, this is not guaranteed to work on all versions of webstart on all\r
- operating systems, and doesn't let you execute Jalview with any\r
- additional parameters.\r
- <p><strong>Running jalview from the InstallAnywhere\r
- installation</strong></p>\r
- <p>If you install with InstallAnywhere you can use several more commands. \r
- However, if you call the application with the link provided by InstallAnywhere \r
- any output from the application will be sent to output.txt, not standard \r
- out.<br>\r
- The jalview application also requires a number of additional\r
- libraries on the class path. The command line below adds the Jalview\r
- installation's 'lib' directory to the list of directories that are\r
- searched for jars to be added to the classpath:</p>\r
-<pre>java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE] </pre>\r
- <p>Use '-help' to get more information on the <a\r
- href="clarguments.html">command line arguments</a> that Jalview\r
- accepts.</p>\r
- <p> </p>\r
- <p> </p>\r
- </body>\r
- </html>\r
+<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
+ *
+ * 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.
+ *
+ * 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/>.
+-->
+<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