+ <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>
+
+
+ <p>There are some important differences between the using the launching script and launching Jalview from its icon:
+ </p>
+ <ul>
+ <li>The launching script will NOT perform automatic updates.</li>
+ <li>The launching script cannot open or use JVL files.</li>
+ </ul>
+
+ <em><strong>Adding the launch script to your path</strong></em>
+ <p>
+ If typing 'jalview' in the terminal prompt (or windows command line)
+ doesn't work then you will need to add the location of the jalview
+ launch script to your
+ <code>PATH</code>.</p><p>
+ How you do this depends on your operating system.
+ </p>
+
+ <ul>
+
+ <li>
+ <p><em>In <strong>Linux</strong> or <strong>Unix</strong> (<code>jalview.sh</code>)</em></p>
+ <p>Running the Linux installer will give you the option of adding a symbolic link to
+ that script in your <code>$PATH</code>, if it finds a suitable place that your user can add such a
+ link (e.g. <code>~/bin</code>, <code>~/.local/bin</code>, <code>~/local/bin</code>, <code>~/opt/bin</code>). If you chose that option then
+ you should be able to launch Jalview on the command line with the simple command
+ <pre>jalview</pre>
+ If you didn't choose that option during installation (or used an earlier version installer), or wish to make another symbolic link, you can link to the
+ launching shell script with the command
+ <pre>ln -s /PATH_TO_JALVIEW/bin/jalview.sh jalview</pre>
+ or you could add <code>/PATH_TO_JALVIEW/bin</code> to your own <code>$PATH</code> as it already contains a symbolic link <code>jalview</code>.
+ </li>
+
+ <li>
+ <p><em>In <strong>Windows</strong> (<code>jalview.bat</code>, <code>jalview.ps1</code>)</em></p>
+ <p>The Windows installer will give you the option of adding Jalview's script folder to your <code>%PATH%</code> allowing you to launch Jalview
+ in a Command Prompt simply with the command
+ <pre>jalview</pre>
+ If you didn't choose that option during installation (or used an earlier version installer), you can either
+ </p>
+ <ul>
+ <li>
+ add the <code>\PATH_TO_JALVIEW\bin</code> folder to your <code>%PATH%</code>, or
+ </li>
+ <li>
+ run the launcher script on the command line with its full path
+ <pre>\PATH_TO_JALVIEW\bin\jalview.bat</pre>
+ (you can leave off the <code>.bat</code> extension if you want).
+ </li>
+ </ul>
+ The <code>jalview.bat</code> file is a generic wrapper around the
+ PowerShell script <code>jalview.ps1</code> in the same folder. This PowerShell script should work with both
+ PowerShell 5.x (which is installed by default on all modern Windows machines), and also PowerShell 6.0+
+ which might have been installed afterwards.
+ </li>
+
+ <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>. <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.
+ </li>
+
+ </ul>
+-->
+ <p><strong><a name="olderinstalls">Older versions of Jalview</a></strong></p>
+
+ <p>
+ If you are using a version of Jalview prior to 2.11.2, you can still launch from the command line, but you will have to
+ use a more platform specific way to launch and use command line arguments.
+
+ <ul>
+ <li>Standard installation on Linux/Unix:
+ <pre>/PATH_TO_JALVIEW/Jalview -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
+ </li>
+ <li>Standard installation on Windows:
+ <pre>\PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa</pre>
+ </li>
+ <li>OSX Application:
+ <pre>open /Applications/Jalview.app --args -open /FULL/PATH/TO/myalignment.fa</pre>
+ <em>(put all the Jalview arguments <em>after</em> the --args parameter, and note that <strong>all files must be specified with their full paths</strong>)</em>
+ <br />
+ <br /></li>
+ <li>Jalview standalone executable Jar<pre>
+ <Path to Java home>/bin/java -jar <Path to Jalview Jar>/jalview-all-1.8.jar -open myalignment.fa</pre></li>
+ </ul>
+ <p>
+ If you have installed Jalview via <em>conda</em> or another package
+ manager then you most likely have a 'jalview' command available in
+ your terminal shell's default path. Alternately, if you have built
+ Jalview from source, then take a look at the doc/building.md file
+ included in the source distribution.