cd jalview
gradle shadowJar
# run
-java -jar build/libs/jalview-all-11.jar
+java -jar build/libs/jalview-all-*-j11.jar
# and/or create launcher
gradle getdown
<p>The method here is described in terms of using a command line. You can easily do this on linux or in a Terminal window in macOS. You can do it in Windows.</p>
<ul>
<li>Java 11 compliant JDK</li>
-<li>gradle 5.2 or above</li>
+<li>gradle 5.2 or above <em>(NB gradle 6.6 and above currently produces NullPointerExceptions during the build. This is non-fatal and does not affect the build. Use gradle 6.5.1 to avoid this)</em></li>
<li>git</li>
</ul>
<blockquote>
and all of the supporting libraries in <code>j11lib/*.jar</code> merged into one <code>.jar</code> archive
file. A default launching class (<code>MAIN-CLASS: jalview.bin.Launcher</code>) is specified in the <code>.jar</code>
manifest file (<code>META/MANIFEST.MF</code>) so a start class doesn't need to be specified.</p>
-<p>Build the shadow jar file in <code>build/lib/jalview-all-11.jar</code> with</p>
+<p>Build the shadow jar file in <code>build/libs/jalview-all-VERSION-j11.jar</code> with</p>
<pre><code class="language-bash">gradle shadowJar
</code></pre>
-<p>and run it with</p>
-<pre><code class="language-bash">java -jar build/lib/jalview-all-11.jar
+<p><strong>NB</strong> <code>VERSION</code> will be replaced with a version number or "<code>DEVELOPMENT</code>" or "<code>TEST</code>" depending on how the branch is set up.</p>
+<p>Run it with</p>
+<pre><code class="language-bash">java -jar build/libs/jalview-all-VERSION-j11.jar
</code></pre>
<p>Because no arguments are required, most OSes will associate a <code>.jar</code> file with the
<code>java</code> application (if this has been installed through the OS and not just a local
-unzip) as a <code>-jar</code> argument so you may find you can launch <code>jalview-all-11.jar</code>
+unzip) as a <code>-jar</code> argument so you may find you can launch <code>jalview-all-VERSION-j11.jar</code>
just by double-clicking on it)!</p>
<blockquote>
<p>The <code>shadowJar</code> task is not a requirement for any other task, so to build the shadow
<p>We develop in Eclipse, and support settings to develop and save Jalview source code
in our preferred style. We also support running the Jalview application, debugging
and running tests with TestNG from within Eclipse.</p>
-<p>To get Jalview set up as a project in Eclipse, we recommend using at least the 2019-12
+<p>To get Jalview set up as a project in Eclipse, we recommend using at least the 2020-03
version of Eclipse IDE for Java Developers which you can download from the Eclipse
website: <a href="https://www.eclipse.org/downloads/">https://www.eclipse.org/downloads/</a>. Since Eclipse 2020-03 you are encouraged to use the Eclipse Installer (see the Eclipse Downloads page).
In the installer, when given a choice of packages for Eclipse you should choose the "Eclipse IDE for Enterprise Java Developers" package.</p>
</ol>
<blockquote>
<p>At time of writing, TestNG for Eclipse does not show up in the Eclipse Marketplace
-as the latest released version does not install in Eclipse 2019-03.
+as the latest released version does not install in Eclipse 2020-03.
However, you can install a working release of TestNG for Eclipse by going to</p>
<p>Help->Install New Software...</p>
<p>and entering</p>
<h3 id="importing-jalview-as-an-eclipse-project"><a href="#importing-jalview-as-an-eclipse-project" name="importing-jalview-as-an-eclipse-project" class="anchor"><span class="octicon octicon-link"></span>Importing Jalview as an Eclipse project</a></h3>
<h4 id="importing-an-already-downloaded-git-repo"><a href="#importing-an-already-downloaded-git-repo" name="importing-an-already-downloaded-git-repo" class="anchor"><span class="octicon octicon-link"></span>Importing an already downloaded git repo</a></h4>
<p>If you have already downloaded Jalview using <code>git clone</code> then you can import this folder into Eclipse directly.</p>
+<p><strong>Before importing the cloned git repo you must create the Eclipse project files.</strong> You can do this by either running</p>
+<p><code>gradle eclipse</code></p>
+<p>or</p>
+<p>Unzipping the file <code>utils/eclipse/eclipse_startup_files.zip</code> in the base repo directory (<code>jalview</code>)</p>
<p>It is important to import
Jalview as a Gradle project (not as a Java project), so go to</p>
<p>File->Import...</p>
git://source.jalview.org / jalview.git / blobdiff