X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fcommandline.html;h=381478f0d7358e6f7a6a112abbd3937d2abaec1e;hb=d5bd34eb49f43735e240058f8875ab0bfcae4441;hp=92d9323e8fc36c3bbab96e30462084c55c731c0a;hpb=44d68d55d9c85bf7b28853feeebc4b901c4a8392;p=jalview.git

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--- a/help/help/html/features/commandline.html
+++ b/help/help/html/features/commandline.html
@@ -26,39 +26,182 @@
   <p>
     <strong>Running Jalview from the command line</strong>
   </p>
-  <p>Jalview is most easily run from the command line if you have
-    built it from source, or via the 'Jalview' executable created from
-    the InstallAnywhere Jalview installation. Both of these mechanisms
-    allow true command line execution of Jalview - allowing you to
-    provide additional options.</p>
-  <p>The Java Webstart version of Jalview can be executed from the
-    command line using something like :
-  <pre>javaws http://www.jalview.org/webstart/jalview.jnlp -open
- <em>yourFileName</em>
-  </pre>
-  But, this is not guaranteed to work on all versions of webstart on all
-  operating systems, and doesn't let you execute Jalview with any
-  additional parameters.
   <p>
-    <strong>Running Jalview from the InstallAnywhere
-      installation</strong>
+    Jalview can be run from the command line, and provides a <a
+      href="clarguments.html">range of arguments</a>.
   </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>
-    If you install with InstallAnywhere you can use several more
-    commands. However, if you call the application with the link
-    provided by InstallAnywhere any output from the application will be
-    sent to output.txt, not standard out.<br> The Jalview
-    application also requires a number of additional libraries on the
-    class path. The command line below adds all the jar files in the
-    Jalview installation's 'lib' directory to the classpath, as well as
-    the Jalview application jar file:
+    <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
+			&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.
+  </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>
+        &lt;Path to Java home&gt;/bin/java -jar &lt;Path to Jalview Jar&gt;/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.
   </p>
-  <pre>java -classpath "$INSTALL_DIR$/lib/*:$INSTALL_DIR$/jalview.jar" jalview.bin.Jalview -open [FILE] </pre>
   <p>
     Use '-help' to get more information on the <a
-      href="clarguments.html">command line arguments</a> that
-    Jalview accepts.
+      href="clarguments.html">command line arguments</a> that Jalview
+    accepts.
+  </p>
+  <p>
+    <strong>Passing JVM Arguments to Jalview</strong><br /> If you need
+    to modify parameters for Jalview's Java Virtual Machine, or
+    configure system properties, then take a look at the instructions
+    for how to <a href="../memory.html#jvm">setting the JVM's
+      maximum memory</a>.<br /> 
+  <p>
+    <strong>Changing Jalview's 'Look and Feel'</strong> <br />If you
+    are experiencing issues with the font size or layout of Jalview's
+    GUI, you can try changing Jalview's 'Look and feel' by
+    specifying a custom system property 'laf' on startup (see <a
+      href="../memory.html#jvm">setting the JVM's memory</a> for
+    instructions on how to do this for your platform). <br />For the
+    Jalview standalone executable jar, simply provide one of the
+    property settings before the -jar argument
   </p>
+  <ul>
+    <li>-Dlaf=system (default look and feel for the OS)</li>
+    <li>-Dlaf=crossplatform (Java's Metal Look and Feel)</li>
+    <li>-Dlaf=nimbus (Java's alternative Nimbus Look and Feel)</li>
+    <li>-Dlaf=mac (only has an effect on OSX)</li>
+    <li>-Dlaf=gtk (only has an effect on Linux)</li>
+    <li>-Dlaf=metal (force Java's Metal Look and Feel, default on linux)</li>
+    <li>-Dlaf=quaqua (macOS only. Force attempt at old macOS theme)</li>
+    <li>-Dlaf=vaqua (macOS only. Force attempt at modern macOS theme)</li>
+  </ul>
+  The currently configured look and feel is logged to Jalview's console.
+  Once the look and feel has been changed, it will be stored in
+  Jalview's .jalview_properties file for future Jalview sessions.  This property is <strong>PREFERRED_LAF</strong> and can also be used to set the Look and feel by editing your .jalview_properties file.
+
   <p>&nbsp;</p>
   <p>&nbsp;</p>
 </body>