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+ <title>Building Jalview from Source</title>
<title>Building Jalview from Source</title>
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+}
+
+body {
+ -webkit-text-size-adjust: 100%;
+ text-size-adjust: 100%;
+ color: #333;
+ font-family: "Helvetica Neue", Helvetica, "Segoe UI", Arial, freesans, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol";
+ font-size: 16px;
+ line-height: 1.6;
+ word-wrap: break-word;
+ width: 728px;
+ max-width: 99%;
+ box-sizing: border-box;
+ padding: 30px 30px 8rem 30px;
+ margin-left: auto;
+ margin-right: auto;
+}
+
+body a {
+ background-color: transparent;
+}
+
+body a:active,
+body a:hover {
+ outline: 0;
+}
+
+body strong {
+ font-weight: bold;
+}
+
+body h1 {
+ font-size: 2em;
+ margin: 0.67em 0;
+}
+
+body img {
+ border: 0;
+}
+
+body hr {
+ box-sizing: content-box;
+ height: 0;
+}
+
+body pre {
+ overflow: auto;
+}
+
+body code,
+body kbd,
+body pre {
+ font-family: monospace, monospace;
+ font-size: 1em;
+}
+
+body input {
+ color: inherit;
+ font: inherit;
+ margin: 0;
+}
+
+body html input[disabled] {
+ cursor: default;
+}
+
+body input {
+ line-height: normal;
+}
+
+body input[type="checkbox"] {
+ box-sizing: border-box;
+ padding: 0;
+}
+
+body table {
+ border-collapse: collapse;
+ border-spacing: 0;
+}
+
+body td,
+body th {
+ padding: 0;
+}
+
+body * {
+ box-sizing: border-box;
+}
+
+body input {
+ font: 13px / 1.4 Helvetica, arial, nimbussansl, liberationsans, freesans, clean, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol";
+}
+
+body a {
+ color: #4078c0;
+ text-decoration: none;
+}
+
+body a:hover,
+body a:active {
+ text-decoration: underline;
+}
+
+body hr {
+ height: 0;
+ margin: 15px 0;
+ overflow: hidden;
+ background: transparent;
+ border: 0;
+ border-bottom: 1px solid #ddd;
+}
+
+body hr:before {
+ display: table;
+ content: "";
+}
+
+body hr:after {
+ display: table;
+ clear: both;
+ content: "";
+}
+
+body h1,
+body h2,
+body h3,
+body h4,
+body h5,
+body h6 {
+ margin-top: 15px;
+ margin-bottom: 15px;
+ line-height: 1.1;
+}
+
+body h1 {
+ font-size: 30px;
+}
+
+body h2 {
+ font-size: 21px;
+}
+
+body h3 {
+ font-size: 16px;
+}
+
+body h4 {
+ font-size: 14px;
+}
+
+body h5 {
+ font-size: 12px;
+}
+
+body h6 {
+ font-size: 11px;
+}
+
+body blockquote {
+ margin: 0;
+}
+
+body ul,
+body ol {
+ padding: 0;
+ margin-top: 0;
+ margin-bottom: 0;
+}
+
+body ol ol,
+body ul ol {
+ list-style-type: lower-roman;
+}
+
+body ul ul ol,
+body ul ol ol,
+body ol ul ol,
+body ol ol ol {
+ list-style-type: lower-alpha;
+}
+
+body dd {
+ margin-left: 0;
+}
+
+body code {
+ font-family: Consolas, "Liberation Mono", Menlo, Courier, monospace;
+ font-size: 12px;
+}
+
+body pre {
+ margin-top: 0;
+ margin-bottom: 0;
+ font: 12px Consolas, "Liberation Mono", Menlo, Courier, monospace;
+}
+
+body .select::-ms-expand {
+ opacity: 0;
+}
+
+body .octicon {
+ font: normal normal normal 16px/1 octicons-link;
+ display: inline-block;
+ text-decoration: none;
+ text-rendering: auto;
+ -webkit-font-smoothing: antialiased;
+ -moz-osx-font-smoothing: grayscale;
+ -webkit-user-select: none;
+ -moz-user-select: none;
+ -ms-user-select: none;
+ user-select: none;
+}
+
+body .octicon-link:before {
+ content: '\f05c';
+}
+
+body:before {
+ display: table;
+ content: "";
+}
+
+body:after {
+ display: table;
+ clear: both;
+ content: "";
+}
+
+body>*:first-child {
+ margin-top: 0 !important;
+}
+
+body>*:last-child {
+ margin-bottom: 0 !important;
+}
+
+body a:not([href]) {
+ color: inherit;
+ text-decoration: none;
+}
+
+body .anchor {
+ display: inline-block;
+ padding-right: 2px;
+ margin-left: -18px;
+}
+
+body .anchor:focus {
+ outline: none;
+}
+
+body h1,
+body h2,
+body h3,
+body h4,
+body h5,
+body h6 {
+ margin-top: 1em;
+ margin-bottom: 16px;
+ font-weight: bold;
+ line-height: 1.4;
+}
+
+body h1 .octicon-link,
+body h2 .octicon-link,
+body h3 .octicon-link,
+body h4 .octicon-link,
+body h5 .octicon-link,
+body h6 .octicon-link {
+ color: #000;
+ vertical-align: middle;
+ visibility: hidden;
+}
+
+body h1:hover .anchor,
+body h2:hover .anchor,
+body h3:hover .anchor,
+body h4:hover .anchor,
+body h5:hover .anchor,
+body h6:hover .anchor {
+ text-decoration: none;
+}
+
+body h1:hover .anchor .octicon-link,
+body h2:hover .anchor .octicon-link,
+body h3:hover .anchor .octicon-link,
+body h4:hover .anchor .octicon-link,
+body h5:hover .anchor .octicon-link,
+body h6:hover .anchor .octicon-link {
+ visibility: visible;
+}
+
+body h1 {
+ padding-bottom: 0.3em;
+ font-size: 1.75em;
+ line-height: 1.2;
+}
+
+body h1 .anchor {
+ line-height: 1;
+}
+
+body h2 {
+ padding-bottom: 0.3em;
+ font-size: 1.5em;
+ line-height: 1.225;
+}
+
+body h2 .anchor {
+ line-height: 1;
+}
+
+body h3 {
+ font-size: 1.25em;
+ line-height: 1.43;
+}
+
+body h3 .anchor {
+ line-height: 1.2;
+}
+
+body h4 {
+ font-size: 1em;
+}
+
+body h4 .anchor {
+ line-height: 1.2;
+}
+
+body h5 {
+ font-size: 1em;
+}
+
+body h5 .anchor {
+ line-height: 1.1;
+}
+
+body h6 {
+ font-size: 1em;
+ color: #777;
+}
+
+body h6 .anchor {
+ line-height: 1.1;
+}
+
+body p,
+body blockquote,
+body ul,
+body ol,
+body dl,
+body table,
+body pre {
+ margin-top: 0;
+ margin-bottom: 16px;
+}
+
+body hr {
+ height: 4px;
+ padding: 0;
+ margin: 16px 0;
+ background-color: #e7e7e7;
+ border: 0 none;
+}
+
+body ul,
+body ol {
+ padding-left: 2em;
+}
+
+body ul ul,
+body ul ol,
+body ol ol,
+body ol ul {
+ margin-top: 0;
+ margin-bottom: 0;
+}
+
+body li>p {
+ margin-top: 16px;
+}
+
+body dl {
+ padding: 0;
+}
+
+body dl dt {
+ padding: 0;
+ margin-top: 16px;
+ font-size: 1em;
+ font-style: italic;
+ font-weight: bold;
+}
+
+body dl dd {
+ padding: 0 16px;
+ margin-bottom: 16px;
+}
+
+body blockquote {
+ padding: 0 15px;
+ color: #777;
+ border-left: 4px solid #ddd;
+}
+
+body blockquote>:first-child {
+ margin-top: 0;
+}
+
+body blockquote>:last-child {
+ margin-bottom: 0;
+}
+
+body table {
+ display: block;
+ width: 100%;
+ overflow: auto;
+ word-break: normal;
+ word-break: keep-all;
+}
+
+body table th {
+ font-weight: bold;
+}
+
+body table th,
+body table td {
+ padding: 6px 13px;
+ border: 1px solid #ddd;
+}
+
+body table tr {
+ background-color: #fff;
+ border-top: 1px solid #ccc;
+}
+
+body table tr:nth-child(2n) {
+ background-color: #f8f8f8;
+}
+
+body img {
+ max-width: 100%;
+ box-sizing: content-box;
+ background-color: #fff;
+}
+
+body code {
+ padding: 0;
+ padding-top: 0;
+ padding-bottom: 0;
+ margin: 0;
+ font-size: 85%;
+ background-color: rgba(0,0,0,0.04);
+ border-radius: 3px;
+}
+
+body code:before,
+body code:after {
+ letter-spacing: -0.2em;
+ content: "\00a0";
+}
+
+body pre>code {
+ padding: 0;
+ margin: 0;
+ font-size: 100%;
+ word-break: normal;
+ white-space: pre;
+ background: transparent;
+ border: 0;
+}
+
+body .highlight {
+ margin-bottom: 16px;
+}
+
+body .highlight pre,
+body pre {
+ padding: 16px;
+ overflow: auto;
+ font-size: 85%;
+ line-height: 1.45;
+ background-color: #f7f7f7;
+ border-radius: 3px;
+}
+
+body .highlight pre {
+ margin-bottom: 0;
+ word-break: normal;
+}
+
+body pre {
+ word-wrap: normal;
+}
+
+body pre code {
+ display: inline;
+ max-width: initial;
+ padding: 0;
+ margin: 0;
+ overflow: initial;
+ line-height: inherit;
+ word-wrap: normal;
+ background-color: transparent;
+ border: 0;
+}
+
+body pre code:before,
+body pre code:after {
+ content: normal;
+}
+
+body kbd {
+ display: inline-block;
+ padding: 3px 5px;
+ font-size: 11px;
+ line-height: 10px;
+ color: #555;
+ vertical-align: middle;
+ background-color: #fcfcfc;
+ border: solid 1px #ccc;
+ border-bottom-color: #bbb;
+ border-radius: 3px;
+ box-shadow: inset 0 -1px 0 #bbb;
+}
+
+body .pl-c {
+ color: #969896;
+}
+
+body .pl-c1,
+body .pl-s .pl-v {
+ color: #0086b3;
+}
+
+body .pl-e,
+body .pl-en {
+ color: #795da3;
+}
+
+body .pl-s .pl-s1,
+body .pl-smi {
+ color: #333;
+}
+
+body .pl-ent {
+ color: #63a35c;
+}
+
+body .pl-k {
+ color: #a71d5d;
+}
+
+body .pl-pds,
+body .pl-s,
+body .pl-s .pl-pse .pl-s1,
+body .pl-sr,
+body .pl-sr .pl-cce,
+body .pl-sr .pl-sra,
+body .pl-sr .pl-sre {
+ color: #183691;
+}
+
+body .pl-v {
+ color: #ed6a43;
+}
+
+body .pl-id {
+ color: #b52a1d;
+}
+
+body .pl-ii {
+ background-color: #b52a1d;
+ color: #f8f8f8;
+}
+
+body .pl-sr .pl-cce {
+ color: #63a35c;
+ font-weight: bold;
+}
+
+body .pl-ml {
+ color: #693a17;
+}
+
+body .pl-mh,
+body .pl-mh .pl-en,
+body .pl-ms {
+ color: #1d3e81;
+ font-weight: bold;
+}
+
+body .pl-mq {
+ color: #008080;
+}
+
+body .pl-mi {
+ color: #333;
+ font-style: italic;
+}
+
+body .pl-mb {
+ color: #333;
+ font-weight: bold;
+}
+
+body .pl-md {
+ background-color: #ffecec;
+ color: #bd2c00;
+}
+
+body .pl-mi1 {
+ background-color: #eaffea;
+ color: #55a532;
+}
+
+body .pl-mdr {
+ color: #795da3;
+ font-weight: bold;
+}
+
+body .pl-mo {
+ color: #1d3e81;
+}
+
+body kbd {
+ display: inline-block;
+ padding: 3px 5px;
+ font: 11px Consolas, "Liberation Mono", Menlo, Courier, monospace;
+ line-height: 10px;
+ color: #555;
+ vertical-align: middle;
+ background-color: #fcfcfc;
+ border: solid 1px #ccc;
+ border-bottom-color: #bbb;
+ border-radius: 3px;
+ box-shadow: inset 0 -1px 0 #bbb;
+}
+
+body .task-list-item {
+ list-style-type: none;
+}
+
+body .task-list-item+.task-list-item {
+ margin-top: 3px;
+}
+
+body .task-list-item input {
+ margin: 0 0.35em 0.25em -1.6em;
+ vertical-align: middle;
+}
+
+body :checked+.radio-label {
+ z-index: 1;
+ position: relative;
+ border-color: #4078c0;
+}
+</style>
</head>
-<body>
-<div id="TOC">
+ <body>
+<ul>
<ul>
-<li><a href="#building-jalview-from-source">Building Jalview from Source</a><ul>
+<li><a href="#setting-up">Setting up</a>
<li><a href="#tldr">tl;dr</a></li>
-<li><a href="#setting-up">Setting up</a><ul>
+<li><a href="#java-11-compliant-jdk">Java 11 compliant JDK</a></li>
<li><a href="#java-11-compliant-jdk">Java 11 compliant JDK</a></li>
<li><a href="#gradle-and-git">gradle and git</a></li>
-</ul></li>
-<li><a href="#downloading-the-jalview-source-tree">Downloading the Jalview source tree</a><ul>
+</li>
+<li><a href="#downloading-the-jalview-source-tree">Downloading the Jalview source tree</a>
<li><a href="#whats-in-the-source-tree">What's in the source tree?</a></li>
-</ul></li>
-<li><a href="#building-jalview">Building Jalview</a><ul>
+<li><a href="#whats-in-the-source-tree">What's in the source tree?</a></li>
+</ul>
<li><a href="#minimal-jalview-build">Minimal Jalview Build</a></li>
<li><a href="#jalview-in-a-jar-file">Jalview in a Jar File</a></li>
<li><a href="#distributed-jar-files">Distributed Jar Files</a></li>
<li><a href="#building-the-getdown-launcher">Building the <code>getdown</code> launcher</a></li>
<li><a href="#running-tests">Running tests</a></li>
<li><a href="#installer-packaging-with-install4j">Installer packaging with <em>install4j</em></a></li>
-</ul></li>
+<li><a href="#building-the-getdown-launcher">Building the <code>getdown</code> launcher</a></li>
<li><a href="#gradle-properties">Gradle properties</a></li>
<li><a href="#enabling-code-coverage-with-openclover">Enabling Code Coverage with OpenClover</a></li>
-<li><a href="#setting-up-in-eclipse-ide">Setting up in Eclipse IDE</a><ul>
+</ul>
<li><a href="#installing-eclipse-ide">Installing Eclipse IDE</a></li>
<li><a href="#importing-jalview-as-an-eclipse-project">Importing Jalview as an Eclipse project</a></li>
-</ul></li>
-</ul></li>
+<li><a href="#enabling-code-coverage-with-openclover">Enabling Code Coverage with OpenClover</a></li>
+<li><a href="#setting-up-in-eclipse-ide">Setting up in Eclipse IDE</a>
</ul>
-</div>
-<h1 id="building-jalview-from-source">Building Jalview from Source</h1>
-<h2 id="tldr">tl;dr</h2>
+</li>
+</ul>
+<h1 id="building-jalview-from-source"><a href="#building-jalview-from-source" name="building-jalview-from-source" class="anchor"><span class="octicon octicon-link"></span>Building Jalview from Source</a></h1>
+</head>
+<pre><code># download
+git clone http://source.jalview.org/git/jalview.git
+<ul>
+cd jalview
+<li><a href="#tldr">tl;dr</a></li>
+# run
+<li><a href="#java-11-compliant-jdk">Java 11 compliant JDK</a></li>
+<li><a href="#gradle-and-git">gradle and git</a></li>
+# and/or create launcher
+gradle getdown
+<li><a href="#whats-in-the-source-tree">What's in the source tree?</a></li>
+cd getdown/files
+java -jar getdown-launcher.jar . jalview
+<li><a href="#minimal-jalview-build">Minimal Jalview Build</a></li>
+<li><a href="#jalview-in-a-jar-file">Jalview in a Jar File</a></li>
+<li><a href="#distributed-jar-files">Distributed Jar Files</a></li>
+<li><a href="#single-shadow-jar-file">Single <em>shadow</em> Jar File</a></li>
+<li><a href="#building-the-getdown-launcher">Building the <code>getdown</code> launcher</a></li>
+<li><a href="#running-tests">Running tests</a></li>
+<li><a href="#installer-packaging-with-install4j">Installer packaging with <em>install4j</em></a></li>
+<li>Java 11 compliant JDK</li>
+<li><a href="#gradle-properties">Gradle properties</a></li>
+<li><a href="#enabling-code-coverage-with-openclover">Enabling Code Coverage with OpenClover</a></li>
+</ul>
+<li><a href="#installing-eclipse-ide">Installing Eclipse IDE</a></li>
+<li><a href="#importing-jalview-as-an-eclipse-project">Importing Jalview as an Eclipse project</a></li>
+so are known to work). If you need or wish to use different implementations (particularly
+you might need a bespoke JDK if you are on an exotic architecture) then the general
+</ul>
+bytecode with any JDK Java 11+. The resulting bytecode (in particular the shadow jar)
+should be runnable in any JRE Java 1.8+. Remember that because Jalview and the getdown launcher
+are Java bytecode you can build on one system where you might have gradle, and run
<pre><code># download
git clone http://source.jalview.org/git/jalview.git
# compile
cd jalview
gradle shadowJar
# run
-java -jar build/libs/jalview-all-11.jar
+# compile
# 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>
+<p>To get set up using <em>only</em> the Eclipse IDE (<a href="https://www.eclipse.org/">https://www.eclipse.org/</a>) then please see the section <a href="#setting-up-in-eclipse-ide">Setting up in Eclipse IDE</a></p>
<li>git</li>
</ul>
<blockquote>
git://source.jalview.org / jalview.git / blobdiff