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+<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
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