3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 <title>Building Jalview from Source</title>
23 <h1>Building Jalview from Source</h1>
26 You will need the following (hopefully):<br>
28 <li>Java development kit (we used JDK1.5SE but JDK1.6 will work too,
29 and maybe even jikes).</li>
30 <li>Ant (we think 1.5.4 is quite sufficient to use the simple build
33 With any luck, after setting your paths and JAVA_HOME correctly, you
34 just need to change to the Jalview directory and run ant (this works
35 from JBuilder and eclipse too, but NetBeans is a bit trickier).
41 <p><strong>Building a webstart version of jalview</strong></p>
42 Jalview depends on several libraries contained in the libs directory
43 of the distribution. In order to access them, they must all be signed
44 jars - using the same jarsigner key as jalview itself. There is a
45 build target in ant to make the signed jar files in a directory called
46 dist. But first you need to make your own key:
47 <p><strong>Making your own key</strong></p>
49 <p>The ant 'makefulldist' target assumes that a keystore exists in a
50 directory 'keys'. To make a key accessible using the default settings
51 in the build.xml file then make the keys directory and add the
52 jarsigner key with the following :
56 keytool -genkey -keystore keys/.keystore -keypass alignmentisfun
57 -storepass alignmentisfun -alias jalview
58 (you will have to answer some personal questions here)
60 (should eventually generate a Jalview.jnlp file
61 in ./dist along with a set of signed jars using the jalview
66 <h1>using IDEs to build Jalview</h1>
67 <p>The Jalview source distribution includes project definitions for
68 Eclipse, Netbeans and some rather ancient Borland JBuilder .jpx
69 project files. These files should be sufficient to set up basic source
70 folders and build paths, but you will need to ensure that all .jar
71 files in the lib and appletlib directories are added to the build path
72 for your IDE project, and that the 'buildindices' target in Jalview's
73 build.xml is executed with the 'outputDir' ant property set to the
74 directory where the IDE expects to place compiled classes ('classes'
75 directory for eclipse, 'build/classes' for netbeans).</p>
76 <p>Note: It is generally not recommended that you distribute build
77 artefacts that were generated automatically via an IDE's own packaging
78 mechanism (e.g. Netbeans' executable Jar and dependent lib directory).
79 The hand-crafted ant build.xml is (currently) the only officially
80 supported method of building distributable versions of Jalview.</p>
82 <a href="mailto:help@jalview.org">Jalview development team</a>