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The species.txt file that is distributed with IGB is version-controlled as part of the IGB source code repository. To see the latest version of this file, go to https://bitbucket.org/lorainelab/integrated-genome-browser, select the source button, and navigate to the resources folder as shown below.
For developers: This is the "master branch" which we use to create the released versions of IGB you download at BioViz. See also Developing Integrated Genome Browser from the IGB Developers Guide.
How to make a species.txt file for a QuickLoad site
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- Open an editor (Microsoft Word is fine, but you'll need to save the file as a plain text (.txt) file.)
- Type the Latin name for the species, including a subspecies or cultivar designations if appropriate (e.g., Zea mays B73).
- Type TAB
- Type the common name for the species (e.g., maize)
- Type TAB
- Type the IGB genome version prefix you'll use for every genome assembly from this species (e.g., Z_mays_B73)
- Type TAB
- Type the Galaxy/UCSC genome version prefix, if available. You only need to do this if the genome versions version is supported by Galaxy and UCSC and you would like to use open files and data from Galaxy in IGB.
- Repeat the previous steps for all new species you'd like to include in your QuickLoad site.
- Save the file as plain text.
- Place the file in the root directory of your QuickLoad site.