-
- <p>From version 2.11.2, Jalview includes a <strong>launching shell script</strong> which is the recommended way to
- launch an installed Jalview application from the command line. It supports all the <a href="clarguments.html">command line arguments</a>
- that Jalview has previously supported, but makes it easier to launch directly from the command line.</p>
+ <p>There are a few different ways to do this:</p>
+ <ul>
+ <li>Use the <strong>jalview</strong> command that links to a <strong>launch
+ script</strong>. Launch scripts are available if you are running an up to
+ date version of Jalview (at least 2.11.2.0), or have installed
+ Jalview via a package manager (e.g. conda, homebrew, apt).
+ </li>
+ <li>Embed arguments in a <strong>.JVL</strong> file. These
+ files will be opened automatically by the Jalview application when
+ double-clicked in a file browser on Windows and OSX.
+ </li>
+ <li>Execute the Jalview standalone Jar file with an existing
+ Java installation</li>
+ <li>For older versions of Jalview, call the <a href="#olderinstalls">native launch program directly</a>.
+ </ul>
+ <p>
+ <strong><a name="script">Jalview's command line launch
+ script</a></strong>
+ <p>Since version 2.11.2, the Jalview native application includes a <strong>launching shell script</strong>. This is the easiest way to
+ launch an installed Jalview application from the command line. </p><p>To run the <strong>launch script</strong>, simply open a Terminal (or Command prompt on Windows), and type:<pre>
+ jalview</pre>
+