<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
</head>
<body>
<h1>Building Jalview from Source</h1>
-<P>
+<p/>
+
+<p>
+You will need the following:<br/>
+<ul>
+ <li> Obtain: git</li>
+ <li> Build/run: Java Development Kit (JDK). JDK11 is now the recommended platform for developing with Jalview. You can obtain a pre-compiled JDK11 for many platforms from https://adoptopenjdk.net/</li>
+ <li> Build: Gradle 5.1 or later. On linux you can obtain this with your package manager (e.g. <code>sudo yum install gradle</code> or <code>sudo apt install gradle</code> or on macOS with brew with <code>brew install gradle</code></li>
+</ul>
+With any luck, once you check out the Jalview source from git and set your JAVA_HOME and PATH correctly, you just need to change to the <code>jalview</code> directory and run <code>gradle getdown</code>.
+</p>
+
+<h2>Obtaining Jalview</h2>
+<p>This is easiest achieved with git:
+<pre>git clone http://www.jalview.org/git/jalview.git</pre>
+Then you can <code>cd jalview</code> to get into the top level jalview dir.
+
+
+<p>
+<h2>Minimal Jalview build</h2>
+<p>To run Jalview, you just need the jalview classes and the .jar libraries that Jalview depends on.</p>
+
+
+<!--
<p>
You will need the following (hopefully):<br>
<ul>
-<li>Java development kit (JDK1.6 is the recommended platform for developing with Jalview, although JDK1.7 seems to work too!).</li>
-<li>Ant (we think 1.5.4 is quite sufficient to use the simple build
-file supplied, and it seems to work with later versions e.g. 1.7).</li>
+<li>Java development kit (JDK1.8 is now the recommended platform for developing with Jalview.</li>
+<li>Ant (1.7 or later will be needed for some of the jarsigning tools).</li>
</ul>
With any luck, after setting your paths and JAVA_HOME correctly, you
just need to change to the Jalview directory and run ant (this works
-from JBuilder and eclipse too, but NetBeans is a bit trickier).
+from eclipse too, but NetBeans is a bit trickier).
<pre>
ant
</pre>
dist. But first you need to make your own key:
<p><strong>Making your own key</strong></p>
-<p>The ant 'makefulldist' target assumes that a keystore exists in a
-directory 'keys'. To make a key accessible using the default settings
-in the build.xml file then make the keys directory and add the
-jarsigner key with the following :
-</p>
-<pre>
-mkdir keys
-keytool -genkey -keystore keys/.keystore -keypass alignmentisfun
--storepass alignmentisfun -alias jalview
- (you will have to answer some personal questions here)
-ant makedist
- (should eventually generate a Jalview.jnlp file
- in ./dist along with a set of signed jars using the jalview
- key)
-</pre>
-
- <p>
+ <p>The ant 'makefulldist' target assumes that a keystore exists in
+ a directory 'keys'. To make a key accessible using the default
+ settings in the build.xml file then make the keys directory and add
+ the jarsigner key with the following :</p>
+ <pre>mkdir keys</pre>
+ <pre>keytool -genkey -keystore keys/.keystore -keypass alignmentisfun
+ -storepass alignmentisfun -sigalg SHA1withRSA -keyalg RSA -alias jalview</pre>
+ <em>(you will have to answer some personal questions here)</em>
+ <pre>ant makedist -DWebStartLocation="file://.pathtojalviewsource./dist" -Dapplication.codebase="*"</pre>
+ <p>This should eventually generate a jalview.jnlp file in ./dist
+ along with a set of signed jars using the jalview key). In order to
+ test locally via webstart you'll now need to add 'file:/' to your
+ java webstart security exception list. Then:</p>
+ <pre>javaws file://.pathtojalviewsource./dist/jalview.jnlp</pre>
+ <p>Please remember to remove that entry afterwards, since it will leave
+ your system vulnerable to malicious code.
+ </p>
+ <p>
<strong>Building the JalviewLite applet<br>
</strong> The JalviewLite applet is compiled using a subset of the packages in
the src directory (specifically: MCView, and jalview.{datamodel,
mechanism (e.g. Netbeans' executable Jar and dependent lib directory).
The hand-crafted ant build.xml is (currently) the only officially
supported method of building distributable versions of Jalview.</p>
+ -->
<address>
<a href="mailto:help@jalview.org">Jalview development team</a>
</address>