<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>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>