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The following describes how to add a new genome version to the IGB QuickLoad repository and update IGB synonyms.txt.
Get started.
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Command-line utilities you'll need need
- faToTwoBit from UCSC
- twoBitInfo from UCSC
- UNIX wget (not installed by default on Mac but available on most other UNIX systems)
- UNIX sort (should be pre-installed on any UNIX system, including Mac)
Install these in a directory in your PATH.
If you're doing this on a Mac desktop or laptop computer, create a directory called "bin" in your home directory and save all compiled binaries there. Edit your .bash_profile file to include a line like the following to ensure that the shell can find the programs.
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export PATH=.:$HOME/bin:$PATH
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Step-by-step guide to adding a new UCSC genome to IGBQuickLoad
Get the QuickLoad data repo
Check out or update a copy of IGB QuickLoad data and source code directories.
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$ svn co https://svn.transvar.org/repos/genomes/pub/quickload quickload
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If you already have a copy, just update using svn up.
Open a Web browser and find the genome you would like to add in the Table Browser at UCSC
Go to http://genome.ucsc.edu/cgi-bin/hgTables