+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
-<head>
-<title>Building Jalview from Source</title>
-</head>
-<body>
-<h1>Building Jalview from Source</h1>
-<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 (JDK1.8 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 eclipse too, but NetBeans is a bit trickier).
-<pre>
- ant
-</pre>
-
-</p>
-<p><strong>Building a webstart version of jalview</strong></p>
-Jalview depends on several libraries contained in the libs directory
-of the distribution. In order to access them, they must all be signed
-jars - using the same jarsigner key as jalview itself. There is a
-build target in ant to make the signed jar files in a directory called
-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</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,
- analysis, appletgui, utils, schemes, api, structure}, and
- com.stevesoft.*). Once compiled, these class files are obfuscated to
- make the code run efficiently. To compile the applet Jar, use the
- makeApplet task - optionally passing in a 'donotobfuscate' property to
- the ant build (e.g. -Ddonotobfuscate=true) to disable obfuscation. </p><p>
- The ant target 'pubapplet' can be used to compile install the
- jalviewApplet.jar and any dependent jars (under appletlib) into a copy
- of the examples directory created under the <em>outputDir</em> build
- property (which defaults to the 'dist' directory).
- </p>
- <p>
-<h1>using IDEs to build Jalview</h1>
- <p>The Jalview source distribution includes project definitions for
- Eclipse, Netbeans and some rather ancient Borland JBuilder .jpx
- project files. These files should be sufficient to set up basic source
- folders and build paths, but you will need to ensure that all .jar
- files in the lib and appletlib directories are added to the build path
- for your IDE project, and that the 'buildindices' target in Jalview's
- build.xml is executed with the 'outputDir' ant property set to the
- directory where the IDE expects to place compiled classes ('classes'
- directory for eclipse, 'build/classes' for netbeans).</p>
- <p>Note: It is generally not recommended that you distribute build
- artefacts that were generated automatically via an IDE's own packaging
- 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>
-</body>
-</html>
git://source.jalview.org / jalview.git / blobdiff