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1 aloraine 3 <html>
2     <title>Integrated Genome Browser QuickLoad Site</title>
3     <body>
4 aloraine 178 <h1>Welcome to IGB Quickload Main</h1>
5 aloraine 3 <p>
6     Data available here are configured for visualization
7     in the <a href="https://bioviz.org">Integrated Genome Browser</a>.
8 aloraine 178 These data include gene annotation files and genome information for
9     many plant, animal, and microbial species.</p>
10     <p>When IGB launches, it contacts a deployed copy of Quickload Main and retrieves
11     a file "<a href="./contents.txt">contents.txt</a>" that lists all genome assemblies available for
12     display in IGB.
13 aloraine 3 </p>
14 aloraine 178 <p>
15     The data here are version-controlled using subversion, a centralized version-control system that
16     attaches versions to individual files and supports checking out parts of the repository. To browse
17     the subversion repository hosting these data, visit
18     <a href="https://svn.bioviz.org/viewvc/genomes/quickload">https://svn.bioviz.org/viewvc/genomes/quickload/</a>.</p>
19 aloraine 81 <h2>About Quickload</h2>
20 aloraine 3 <p>
21 aloraine 81 A Quickload site is a simple system of directories, sequence files, and
22     annotation files formatted for visualization in Integrated Genome Browser. It's a convenient
23 aloraine 178 way to share data sets with other labs and with the public. IGB can display the contents of
24     many Quickload sites at the same time. This makes it easy to compare data across experiments.
25     This makes IGB an "integrated" genome browser.
26 aloraine 3 </p>
27 aloraine 178 <h2>About this site</h2>
28 aloraine 3 <p>
29 aloraine 178 This site is a checked-out copy of Quickload Main subversion repository, deployed in the "htdocs" directory
30     of the apache2 Web server.
31     </p>
32 aloraine 151 <p>
33 aloraine 178 To make the Quickload data contents easy to browse, the repository also includes styling configurations using
34     javascript and CSS.
35 aloraine 151 </p>
36 aloraine 178
37     <h2>How to get a copy</h2>
38 aloraine 150 <p>Install svn and check out the repository with a read-only user:</p>
39 aloraine 180 <p>`svn co --username=guest https://svn.bioviz.org/repos/genomes/quickload`</p>
40     <p>When prompted, enter username "guest" and password "guest".</p>
41 aloraine 178
42     <h2>Test a checked-out copy in Integrated Genome Browser</h2>
43 aloraine 179 <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 containing the file "contents.txt" is the Quickload root directory.</p>
44 aloraine 178 <h2>Add too big 2bit files</h2>
45     <p>Some genome sequence files are so large that they are not version-controlled. One such file
46     is `T_aestivum_Aug_2018.2bit`, a wheat genome assembly sequence file. To enable IGB users to view
47     sequence data from this genome, add the file to directory `quickload/T_aestivum_Aug_2018`.</p>
48 aloraine 150 <hr/>
49 aloraine 3 </body>
50     </html>

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