genomes/quickload/HEADER.md

<html>
<title>Integrated Genome Browser QuickLoad Site</title>
<body>
<h1>Welcome to IGB Quickload Main</h1>
<p>
Data available here are configured for visualization
in the <a href="https://bioviz.org">Integrated Genome Browser</a>.
These data include gene annotation files and genome information for 
many plant, animal, and microbial species.</p>
<p>When IGB launches, it contacts a deployed copy of Quickload Main and retrieves
a file "<a href="./contents.txt">contents.txt</a>" that lists all genome assemblies available for
display in IGB.
</p>
<p>
The data here are version-controlled using subversion, a centralized version-control system that
attaches versions to individual files and supports checking out parts of the repository. To browse
the subversion repository hosting these data, visit 
<a href="https://svn.bioviz.org/viewvc/genomes/quickload">https://svn.bioviz.org/viewvc/genomes/quickload/</a>.</p>
<h2>About Quickload</h2>
<p>
A Quickload site is a simple system of directories, sequence files, and
annotation files formatted for visualization in Integrated Genome Browser. It's a convenient
way to share data sets with other labs and with the public. IGB can display the contents of
many Quickload sites at the same time. This makes it easy to compare data across experiments.
This makes IGB an "integrated" genome browser. 
</p>
<h2>About this site</h2>
<p>
This site is a checked-out copy of Quickload Main subversion repository, deployed in the "htdocs" directory
of the apache2 Web server. 
 </p>
<p>
To make the Quickload data contents easy to browse, the repository also includes styling configurations using
javascript and CSS. 
</p>

<h2>How to get a copy</h2> 
<p>Install svn and check out the repository with a read-only user:</p>
<p>`svn co --username=guest co https://svn.bioviz.org/repos/genomes/quickload`</p>

<h2>Test a checked-out copy in Integrated Genome Browser</h2>
<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>
<h2>Add too big 2bit files</h2>
<p>Some genome sequence files are so large that they are not version-controlled. One such file
is `T_aestivum_Aug_2018.2bit`, a wheat genome assembly sequence file. To enable IGB users to view
sequence data from this genome, add the file to directory `quickload/T_aestivum_Aug_2018`.</p> 
<hr/>
</body>
</html>
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			<p>`svn co --username=guest co https://svn.bioviz.org/repos/genomes/quickload`</p>
40	aloraine	178
41			<h2>Test a checked-out copy in Integrated Genome Browser</h2>
42			<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>
43			<h2>Add too big 2bit files</h2>
44			<p>Some genome sequence files are so large that they are not version-controlled. One such file
45			is `T_aestivum_Aug_2018.2bit`, a wheat genome assembly sequence file. To enable IGB users to view
46			sequence data from this genome, add the file to directory `quickload/T_aestivum_Aug_2018`.</p>
47	aloraine	150	<hr/>
48	aloraine	3	</body>
49			</html>