<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>
+ <strong><a name="script">Jalview's command line launch</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>
<li>
<p><em>In <strong>macOS</strong> (<code>jalview</code>)</em></p>
- <p>
- We don't currently provide a macOS installer program, so you will need to add the command to you path manually. The script you should use to launch Jalview is linked to as
- <pre>/Applications/Jalview.app/Contents/MacOS/jalview</pre>
- so you can run that command with its full path, or make your own symbolic link to there, or add that folder to your <code>$PATH</code>.
- </p>
- <p>
- If you cannot see the
- <code>jalview</code>
- command in the MacOS directory, then you probably have an older
- Jalview installation. In that case, you should make a symbolic
- link directly to the launch script with the command
- <pre>ln -s /Applications/Jalview.app/Content/Resources/app/bin/jalview.sh jalview</pre>
- <em>If this doens't work, check your installation is running
- Jalview 2.11.2.0 or later.</em>
- </p>
- </li>
+ <p>We don't currently provide a macOS installer program, so you
+ will need to add the command to you path manually. The script you
+ should use to launch Jalview is linked to as
+ <pre>/Applications/Jalview.app/Contents/MacOS/jalview</pre> so you
+ can run that command with its full path, or make your own symbolic
+ link to there, or add that folder to your <code>$PATH</code>. <pre>echo /Applications/Jalview.app/Contents/Resources/app/bin | sudo tee -a /etc/paths.d/Jalview</pre>
+ This adds the directory
+ "/Applications/Jalview.app/Contents/Resources/app/bin/"
+ to a "Jalview" file in the /etc/paths.d/ directory. The
+ lines from all the files in this directory are added the $PATH
+ variable for all shells and users.
+ </p>
+ <p>
+ If you cannot see the
+ <code>jalview</code>
+ command in the MacOS directory, then you probably have an older
+ Jalview installation. In that case, you should make a symbolic link
+ directly to the launch script with the command
+ <pre>ln -s /Applications/Jalview.app/Content/Resources/app/bin/jalview.sh jalview</pre>
+ <em>If this doens't work, check your installation is running
+ Jalview 2.11.2.0 or later.</em>
+ </p>
+ </li>
</ul>
<!-- <p><em>Future</em></p>
A future version of Jalview will include a tool to allow adding these "<code>jalview</code>" links to your <code>PATH</code> automatically.
included in the source distribution.
</p>
<p>
- Use '-help' to get more information on the <a
+ Use '--help' to get more information on the <a
href="clarguments.html">command line arguments</a> that Jalview
accepts.
</p>