@gmod/jbrowse
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JBrowse - client-side genome browser
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class="navGroupCategoryTitle">Configuring tracks</h3><ul><li class="navListItem"><a class="navItem" href="/docs/reference_sequence.html">Reference sequence configuration</a></li><li class="navListItem"><a class="navItem" href="/docs/canvas_features.html">CanvasFeatures</a></li><li class="navListItem"><a class="navItem" href="/docs/html_features.html">HTMLFeatures</a></li><li class="navListItem"><a class="navItem" href="/docs/alignments.html">Alignments tracks</a></li><li class="navListItem"><a class="navItem" href="/docs/bigwig.html">Wiggle/BigWig Tracks</a></li><li class="navListItem"><a class="navItem" href="/docs/variants.html">VCF tracks</a></li><li class="navListItem"><a class="navItem" href="/docs/minimal.html">Minimal JBrowse configurations</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Advanced configuration</h3><ul><li class="navListItem"><a class="navItem" href="/docs/embedding.html">Embedding JBrowse</a></li><li class="navListItem"><a class="navItem" href="/docs/mouse_configs.html">Mouse clicks, menus, and popups</a></li><li class="navListItem"><a class="navItem" href="/docs/configuration_file_formats.html">Configuration File Formats</a></li><li class="navListItem"><a class="navItem" href="/docs/dataset_selector.html">Dataset Selector</a></li><li class="navListItem"><a class="navItem" href="/docs/track_selectors.html">Track Selectors</a></li><li class="navListItem"><a class="navItem" href="/docs/track_metadata.html">Track Metadata</a></li><li class="navListItem"><a class="navItem" href="/docs/global_options.html">Global configuration options</a></li><li class="navListItem"><a class="navItem" href="/docs/compression.html">Compressing JBrowse data</a></li><li class="navListItem"><a class="navItem" href="/docs/authentication.html">HTTP authentication for JBrowse</a></li><li class="navListItem"><a class="navItem" href="/docs/paired_reads.html">Paired read viewing</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Command line</h3><ul><li class="navListItem"><a class="navItem" href="/docs/flatfile-to-json.pl.html">flatfile-to-json.pl</a></li><li class="navListItem"><a class="navItem" href="/docs/remove-track.pl.html">remove-track.pl</a></li><li class="navListItem"><a class="navItem" href="/docs/ucsc-to-json.pl.html">ucsc-to-json.pl</a></li><li class="navListItem"><a class="navItem" href="/docs/generate-names.pl.html">generate-names.pl</a></li><li class="navListItem"><a class="navItem" href="/docs/prepare-refseqs.pl.html">prepare-refseqs.pl</a></li><li class="navListItem"><a class="navItem" href="/docs/biodb-to-json.pl.html">biodb-to-json.pl</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">JBrowse Desktop</h3><ul><li class="navListItem navListItemActive"><a class="navItem" href="/docs/jbrowse_desktop.html">JBrowse Desktop</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">FAQ</h3><ul><li class="navListItem"><a class="navItem" href="/docs/faq.html">JBrowse FAQ</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Other topics</h3><ul><li class="navListItem"><a class="navItem" href="/docs/url_strings.html">JBrowse URL parameters</a></li><li class="navListItem"><a class="navItem" href="/docs/image_tracks.html">Pre-rendered Image Tracks</a></li><li class="navListItem"><a class="navItem" href="/docs/feature_coverage.html">Feature Coverage Tracks</a></li><li class="navListItem"><a class="navItem" href="/docs/screenshots.html">Automating screenshots of JBrowse</a></li><li class="navListItem"><a class="navItem" href="/docs/events.html">JBrowse Subscribe/Publish events</a></li><li class="navListItem"><a class="navItem" href="/docs/perl_config.html">Sample configuration bash script</a></li><li class="navListItem"><a class="navItem" href="/docs/data_formats.html">JBrowse REST API and Data APIs</a></li><li class="navListItem"><a class="navItem" href="/docs/plugins.html">Installing and writing plugins</a></li><li class="navListItem"><a class="navItem" href="/docs/cors.html">Cross-origin resource sharing (CORS)</a></li><li class="navListItem"><a class="navItem" href="/docs/sparql.html">SPARQL configuration</a></li><li class="navListItem"><a class="navItem" href="/docs/data_export.html">Data export</a></li><li class="navListItem"><a class="navItem" href="/docs/usage_stats.html">Usage Statistics</a></li></ul></div></div></section></div><script>
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</script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">JBrowse Desktop</h1></header><article><div><span><p>This page provides a reference guide for "Desktop JBrowse" or "JBrowse
Desktop", which is a <a href="https://electron.atom.io">electron application</a>
that was unveiled for the release of JBrowse 1.12.0.</p>
<p>The operation of JBrowse Desktop is comparable to other desktop genome
browsers like IGV or IGB, and it can be run without setting up a
webserver (most of the time normal jbrowse runs on apache and is viewed
in a web browser). In contrast, JBrowse Desktop is a simple exe file
that can easily be run locally on Windows, Mac OS, or Linux.</p>
<h2><a class="anchor" aria-hidden="true" id="installation"></a><a href="#installation" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Installation</h2>
<p>At the most basic level, to set up JBrowse Desktop:</p>
<ul>
<li>Download a zip file script from jbrowse.org e.g. from the latest release at
<a href="http://jbrowse.org/blog/">http://jbrowse.org/blog/</a>. Linux, Windows, and Darwin variants are
available as <code>JBrowse-1.15.4-desktop-<system>-x64.zip</code>.</li>
<li>After downloading, unzip the file to somewhere. There is no official
installer but you can move it to the Program files or Applications
directory as needed.</li>
</ul>
<p>Note: on Mac, you can alternatively use Homebrew and run `brew cask
install jbrowse` which will download and place jbrowse in your
Application directory</p>
<p>Also note: On Linux, you will need libgconf</p>
<pre><code class="hljs">sudo apt install libgconf-2-4
</code></pre>
<p>See this thread for details <a href="https://github.com/electron/electron/issues/1518">https://github.com/electron/electron/issues/1518</a></p>
<h2><a class="anchor" aria-hidden="true" id="overview-of-jbrowse-desktop"></a><a href="#overview-of-jbrowse-desktop" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Overview of JBrowse Desktop</h2>
<p>When you run JBrowse Desktop you will see a sort of "welcome screen"
that gives you several options</p>
<ul>
<li>View Volvox sample data</li>
<li>Open sequence file, this allows you to open FASTA, Indexed FASTA, or
.2bit</li>
<li>Open data directory, this allows you to open a data directory that
has been prepared with normal jbrowse tools</li>
</ul>
<p>Note: it is highly recommended to use Indexed FASTA (selecting both a
fasta and a fai file generated by `samtools faidx file.fasta`) or
2bit. Even small genomes with normal FASTA will be much slower!</p>
<h2><a class="anchor" aria-hidden="true" id="screenshot"></a><a href="#screenshot" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Screenshot</h2>
<p><img src="/docs/assets/config/Jbrowse_desktop_screenshot.png" alt="800px|center|thumb|JBrowse desktop."></p>
<p>This is the welcome page when you open up the jbrowse app. You can open
up sequence files such as fasta, 2bit, or indexed fasta here. Or, you
can open up a pre-existing jbrowse data directory. You can also see a
list of past "sessions" which can be revisited later. The red warning is
sort of awkward but it does not have any meaning here, it just means
that you aren't currently in jbrowse main screen</p>
<h2><a class="anchor" aria-hidden="true" id="limitations"></a><a href="#limitations" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Limitations</h2>
<ul>
<li>The "Save session" function will not save some configuration
customizations, so if you have advanced customizations it would be
recommended to make a data directory by hand the trackList.json and
tracks.conf format files</li>
<li>If you open a data directory on the web, then "Save session" won't
work</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="features"></a><a href="#features" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Features</h2>
<ul>
<li>Can open files from shared network folders and external hard drives
on both windows and mac</li>
<li>Can open files from remote URLs</li>
<li>Can open data directories from remote URL</li>
<li>Saves "sessions" to the OS "application data" folders</li>
<li>Has a "home screen" that lists previous sessions</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="technical-details"></a><a href="#technical-details" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Technical details</h2>
<p>The folder where sessions are saved is generally</p>
<ul>
<li>OSX - "~/Library/Application Support/jbrowse"</li>
<li>Windows - "C:\Users\username\AppData\Roaming\jbrowse"</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="tested-platforms"></a><a href="#tested-platforms" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Tested platforms</h2>
<ul>
<li>OSX Mavericks</li>
<li>macOS sierra</li>
<li>Windows 7</li>
<li>Windows 10</li>
</ul>
<p>Note: JBrowse Desktop doesn't work on windows XP and Vista (in fact all
electron apps require Windows 7+)</p>
<h1><a class="anchor" aria-hidden="true" id="external-links"></a><a href="#external-links" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>External Links</h1>
<ul>
<li><a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0924-1">JBrowse: a dynamic web platform for genome visualization and
analysis</a>
paper</li>
</ul>
</span></div></article></div><div class="docs-prevnext"><a class="docs-prev button" href="/docs/biodb-to-json.pl.html">← biodb-to-json.pl</a><a class="docs-next button" href="/docs/faq.html">JBrowse FAQ →</a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#installation">Installation</a></li><li><a href="#overview-of-jbrowse-desktop">Overview of JBrowse Desktop</a></li><li><a href="#screenshot">Screenshot</a></li><li><a href="#limitations">Limitations</a></li><li><a href="#features">Features</a></li><li><a href="#technical-details">Technical details</a></li><li><a href="#tested-platforms">Tested platforms</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><h5>Docs</h5><a href="/blog">Blog</a><a href="/docs/tutorial.html">Getting Started</a></div><div><h5>Community</h5><a href="https://gitter.im/GMOD/jbrowse">Project Chat</a><a href="https://twitter.com/JBrowseGossip" target="_blank" rel="noreferrer noopener">Twitter</a></div><div><h5>More</h5><a href="https://github.com/GMOD/jbrowse">GitHub</a><a class="github-button" href="https://github.com/GMOD/jbrowse" data-icon="octicon-star" data-count-href="/GMOD/jbrowse/stargazers" data-show-count="true" data-count-aria-label="# stargazers on GitHub" aria-label="Star this project on GitHub">Star</a></div></section><section class="copyright">Copyright © 2019 Evolutionary Software Foundation</section></footer></div></body></html>