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Fri Sep 15 15:43:45 2023 UTC (9 months, 1 week ago) by aloraine
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1 <html>
2 <title>Integrated Genome Browser QuickLoad Site</title>
3 <body>
4 <h1>Welcome to IGB Quickload Main</h1>
5 <p>
6 Data available here are configured for visualization
7 in the <a href="https://bioviz.org">Integrated Genome Browser</a>.
8 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 </p>
14 <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 <h2>About Quickload</h2>
20 <p>
21 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 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 </p>
27 <h2>About this site</h2>
28 <p>
29 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 <p>
33 To make the Quickload data contents easy to browse, the repository also includes styling configurations using
34 javascript and CSS.
35 </p>
36
37 <h2>How to get a copy</h2>
38 <p>Install svn and check out the repository with a read-only user:</p>
39 <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
42 <h2>Test a checked-out copy in Integrated Genome Browser</h2>
43 <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 <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 <hr/>
49 </body>
50 </html>

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