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- simple meta-data files describing available genome versions, annotswhat the QuickLoad site contains
- data files, including sequence data, alignments, genome graphs, and annotations
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Create a QuickLoad root directory (folder( ) on your local computer or on a Web server. This folder will contain your genome directories and a "meta-data" file called contents.txt.
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Create genome directories for each of the genome versions you want to make available via QuickLoad.To ensure the genome corresponding to genome versions you want to make available via your QuickLoad.
First, find out if main QuickLoad site already supports your genome of interest. To find out which genome versions are already supported, view http://igbquickload.org/quickload/contents.txt.
The first column of this file lists IGB's names for genome versions and the second column lists a description of that genome. If your genome of interest is listed in this file, then you should create a version directory identical to the value in the first column. In QuickLoad, IGB genome version names are also the name of the genome version directories. So if you look at the directories listed in the main IGBQuickLoad site root directory, you'll see a directory (folder) for every genome version listed in the main site's contents.txt.
For example, if your QuickLoad site contains data for the latest human genome and no other genomes, then you should make a directory named H_sapiens_Dec_2013, which is also IGB's synonym for the version of the human genome that was released December, 2013, also called GRCh38/hg38.
If you're setting up a QuickLoad site for a new (unsupported) genome
If your genome is not listed in http://igbquickload.org/quickload/contents.txt, then you'll need to create your own, IGB-friendly name. Doing this will ensure that your genome version will be displayed correctly in the Current Genome tabbed panel menus, . the names of these directories should follow the IGB format of:
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For example, there are two Oryza sativa (rice) subspecies in wide cultivation: japonica and indica.The first rice sequence published was from the Nipponbare variety which is a member of the japonica subspecies. Because an indica genome sequence is now available, we need names that distinguish them. We distinguish the japonica assemblies using prefix O_sativa_japonica and the month and year of release: O_sativa_japonica_JunOct_20092011. Annotations and sequence data reside in genome version folder O_sativa_japonica_JunOct_2009 2011 on the main IGB QuickLoad site - view its contents by visiting http://igbquickload.org/quickload/O_sativa_japonica_JunOct_20092011
Tip: If you set up your QuickLoad site in the Web directories of an Apache server, you can modify and fine-tune how files are displayed by adding directives to the .htaccess file in that directory. You can configure Apache to allow users to view the contents of your QuickLoad directory and include a short description of each file or data set. Here is an example:
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Options Indexes |
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Step Three: Create contents.txt file listing available genome versions for your QuickLoad site.
Create a simple, plain text file called contents.txt and add it the top-level directory.
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