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<title>Integrated Genome Browser QuickLoad Site</title> |
<title>Integrated Genome Browser QuickLoad Site</title> |
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<body> |
<body> |
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<h1>Welcome to IGB Quickload</h1> |
<h1>Welcome to IGB Quickload Main</h1> |
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<p> |
<p> |
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Data available here are configured for visualization |
Data available here are configured for visualization |
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in the <a href="https://bioviz.org">Integrated Genome Browser</a>. |
in the <a href="https://bioviz.org">Integrated Genome Browser</a>. |
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These data include gene annotation files and genome information for |
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many plant, animal, and microbial species.</p> |
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<p>When IGB launches, it contacts a deployed copy of Quickload Main and retrieves |
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a file "<a href="./contents.txt">contents.txt</a>" that lists all genome assemblies available for |
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display in IGB. |
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</p> |
</p> |
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<p> |
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The data here are version-controlled using subversion, a centralized version-control system that |
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attaches versions to individual files and supports checking out parts of the repository. To browse |
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the subversion repository hosting these data, visit |
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<a href="https://svn.bioviz.org/viewvc/genomes/quickload">https://svn.bioviz.org/viewvc/genomes/quickload/</a>.</p> |
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<h2>About Quickload</h2> |
<h2>About Quickload</h2> |
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<p> |
<p> |
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A Quickload site is a simple system of directories, sequence files, and |
A Quickload site is a simple system of directories, sequence files, and |
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annotation files formatted for visualization in Integrated Genome Browser. It's a convenient |
annotation files formatted for visualization in Integrated Genome Browser. It's a convenient |
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way to share data sets with other labs and with the public. |
way to share data sets with other labs and with the public. IGB can display the contents of |
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many Quickload sites at the same time. This makes it easy to compare data across experiments. |
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This makes IGB an "integrated" genome browser. |
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</p> |
</p> |
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<h2>About this Web site</h2> |
<h2>About this site</h2> |
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<p> |
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This site is a checked-out copy of Quickload Main subversion repository, deployed in the "htdocs" directory |
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of the apache2 Web server. |
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</p> |
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<p> |
<p> |
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This site is a checked-out copy of this <a href="https://svn.bioviz.org/viewvc/genomes/quickload/">subversion repository</a>. |
To make the Quickload data contents easy to browse, the repository also includes styling configurations using |
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javascript and CSS. |
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</p> |
</p> |
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<h2>How to replicate this Web site</h2> |
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<p>Set up a host with the Apache2 Web server. (It may work with other servers, too. We have never tested that.)</p> |
<h2>How to get a copy</h2> |
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<p>Install svn and check out the repository with a read-only user:</p> |
<p>Install svn and check out the repository with a read-only user:</p> |
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<p>`svn co --username=guest co https://svn.bioviz.org/repos/genomes/quickload`</p> |
<p>`svn co --username=guest co https://svn.bioviz.org/repos/genomes/quickload`</p> |
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<p>Place the checkedout-repository in your htdocs directory (DocumentRoot)</p> |
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<p>Configure your Web server to allow fancy directory listings and configurations from .htaccess files residing alongside content.</p> |
<h2>Test a checked-out copy in Integrated Genome Browser</h2> |
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<p>To support IGB 9.1.4 and lower, add `T_aestivum_Aug_2018.2bit` to directory `quickload/T_aestivum_Aug_2018`.</p> |
<p>Open Integrated Genome Browser and select <B>Preferences</B> from the <B>File</B> menu. Select the <B>Data Sources</B> tab. Add the checked-out root directory as a new Quickload Data Source. The folder contain the file "contents.txt" is the Quickload root directory. See examples within IGB itself.</p> |
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<h2>Test it with Integrated Genome Browser</h2> |
<h2>Add too big 2bit files</h2> |
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<p>Open Integrated Genome Browser and select <B>Preferences</B> from the <B>File</B> menu. Select the <B>Data Sources</B> tab. Add your new site as a new Quickload Data Source. The folder contain the file "contents.txt" is the Quickload root directory. See examples within IGB itself.</p> |
<p>Some genome sequence files are so large that they are not version-controlled. One such file |
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is `T_aestivum_Aug_2018.2bit`, a wheat genome assembly sequence file. To enable IGB users to view |
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sequence data from this genome, add the file to directory `quickload/T_aestivum_Aug_2018`.</p> |
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<hr/> |
<hr/> |
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</body> |
</body> |
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</html> |
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