JAL-4104 JAL-4102 update help docs with script to add jalview command line tool to...

diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html
index 2ffe0bc..381478f 100644 (file)
--- a/help/help/html/features/commandline.html
+++ b/help/help/html/features/commandline.html
@@ -109,22 +109,29 @@
   
   <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
+                       &quot;/Applications/Jalview.app/Contents/Resources/app/bin/&quot;
+                       to a &quot;Jalview&quot; 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.