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=e00d390762bba8e732343bb49233cfcfff0894ce;hb=6a05eb3f55d97e685f0c723822384633d5636778;hp=92d9323e8fc36c3bbab96e30462084c55c731c0a;hpb=d113749a183a3ea8f3f7e22c725511f59f1d833f;p=jalview.git

diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html
index 92d9323..e00d390 100644
--- a/help/help/html/features/commandline.html
+++ b/help/help/html/features/commandline.html
@@ -26,38 +26,48 @@
   <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>. These arguments
+    can also be passed via <strong>.JVL</strong> files, which are opened
+    automatically by the Jalview application when double-clicked in a
+    file browser on Windows and OSX.
   </p>
+  The way that you launch Jalview from the command line depends on the
+  platform you are on, and how it has been installed.
+
+  <ul>
+    <li>Standard installation on Linux/Unix:<pre>
+       /PATH_TO_JALVIEW/Jalview -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://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 ~/myalignment.fa</pre><em>(put
+        all the Jalview arguments <em>after</em> the --args parameter)
+    </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 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:
+    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, then take a
+    look at the instructions for how to <a href="../memory.html#jvm">setting
+      the JVM's maximum memory</a>.
   </p>
   <p>&nbsp;</p>
   <p>&nbsp;</p>