X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fcommandline.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Fcommandline.html;h=b16274057a69b0e3cc030bdb34f9eec371fc2dc8;hb=c8d80485038ab96fb06bd0885c323803646d8e57;hp=2ffe0bc02aa9302eeb4bcc4511c10097d70be1f4;hpb=1b1f995b3eb83dc3496510bfc2278f1f72fcfd8a;p=jalview.git

diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html
index 2ffe0bc..b162740 100644
--- a/help/help/html/features/commandline.html
+++ b/help/help/html/features/commandline.html
@@ -46,8 +46,7 @@
       <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>
@@ -109,22 +108,29 @@
   
   <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.
@@ -161,7 +167,7 @@
     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>