@gmod/jbrowse
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JBrowse - client-side genome browser
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</script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">Compressing JBrowse data</h1></header><article><div><span><p>Scripts such as <code>flatfile-to-json.pl</code> and <code>prepare-refseqs.pl</code> offer a <code>--compress</code> option to compress (gzip) feature and sequence data to conserve server disk space and reduce server CPU load even further. Using this option requires some additional web server configuration.</p>
<p>In order to use this functionality</p>
<ul>
<li><code>AllowOverride FileInfo</code> (or <code>AllowOverride All</code>) must be set for the JBrowse data directories in order to use the <code>.htaccess</code> files generated by the formatting scripts.</li>
<li><code>mod_headers</code> must be installed and enabled, and if the web server is using <code>mod_gzip</code> or <code>mod_deflate</code>, <code>mod_setenvif</code> must also be installed and enabled.</li>
</ul>
<p>The reason for these things is that the items jsonz and txtz should not be "double gzipped" and be given proper response headers</p>
<p>For Apache: A configuration snippet like the following should be included in the configuration:</p>
<pre><code class="hljs"> <span class="hljs-section"><IfModule mod_gzip.c></span>
<span class="hljs-attribute">mod_gzip_item_exclude</span> <span class="hljs-string">"(\.jsonz|\.txtz)"</span>
<span class="hljs-section"></IfModule></span>
<span class="hljs-section"><IfModule setenvif.c></span>
<span class="hljs-attribute">SetEnvIf</span> Request_URI <span class="hljs-string">"(\.jsonz|\.txtz)"</span> no-gzip dont-vary
<span class="hljs-section"></IfModule></span>
<span class="hljs-section"><IfModule mod_headers.c></span>
<span class="hljs-section"><FilesMatch "(\.jsonz|\.txtz)"></span>
<span class="hljs-attribute"><span class="hljs-nomarkup">Header</span></span> onsuccess set Content-Encoding gzip
<span class="hljs-section"></FilesMatch></span>
<span class="hljs-section"></IfModule></span>
</code></pre>
<p>For nginx: A configuration snippet like the following should be included in the configuration:</p>
<pre><code class="hljs"> location ~* <span class="hljs-string">"\.(json|txt)z$"</span> {
add_header Content-Encoding gzip;
gzip off;
types { application/json jsonz; }
}
</code></pre>
<h2><a class="anchor" aria-hidden="true" id="newer-jbrowse-versions"></a><a href="#newer-jbrowse-versions" 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>Newer JBrowse versions</h2>
<p>Note that many new data formats that JBrowse supports e.g.</p>
<ul>
<li>BigWig</li>
<li>BAM</li>
<li>GFF3Tabix</li>
<li>BEDTabix</li>
<li>VCFTabix</li>
<li>TwoBit</li>
</ul>
<p>These formats are already compressed and they do not require pre-processing.</p>
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