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The following describes how to add a new genome version to the IGB QuickLoad repository and update IGB species.txt.
Command-line utilities you'll need
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- faToTwoBit from UCSC (needed if there is no 2Bit file available)twoBitInfo from UCSC (needed to generate the genome.txt file)and twoBitInfo scripts from UCSC Jim Kent tools. Available from http://hgdownload.cse.ucsc.edu/admin/exe/
- 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)
- IGBQuickLoad scripts in genomes/pub/src subversion repo.
Compiled UCSC software tools are available from http://hgdownload.cse.ucsc.edu/admin/exe/.
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- A version of git for your platform.
- A version of subversion (svn) for your platform.
- IGBQuickLoad scripts in https://bitbucket.org/lorainelab/genomesource (details on how to get the code are in the next sections)
Get the compiled programs from UCSC and make sure they are executable on your system.
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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For example, the following sequence of commands downloads the software, moves it to a directory named "bin" in the home directory, and then makes it executable using the chmod command.
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wget http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/twoBitInfo mv twoBitInfo ~/bin chmod a+x ~/bin/twoBitInfo |
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cd # change into your home directory svn co https://svn.transvar.org/repos/genomes/trunk/pub/quickload //svn.bioviz.org/repos/genomes/quickload/ |
To ensure you will be able to upload changes, request a user id and password from Dr. Loraine. Alternatively, use user name "guest" and password "guest" for read-only access.
Or, if you already have a copy, just update using svn up. Change into your local copy and run:
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svn up |
This will update everything in the current working directory and all the directories beneath it. To avoid conflicts with other people's committed changes, be sure to update your local copy of IGB QuickLoad repo before starting work.
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You'll need this only if you want to test how the new genome directory looks OK when visited in a Web browser. How you do this will depend on your computer.
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As before, open a terminal and change into the directory where you want your checked-out copy of the genomes src genomesource code to reside. A As described above, a good place for checked-out code is a directory named src in your home directory.
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Then, use git to get a copy of the QuickLoad source code:
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git clone https://bitbucket.org/lorainelab/genomes_srcgenomesource |
To ensure that you'll be able to run the code, add the new directory to your PATH and your PYTHONPATH environmental variables by editing your .bash_profile startup script:
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Now, the basic structure - sequence and meta-data about contigs and chromosomes - is available. Now you need to add the annotations. For this, see:
Updating mRNA, EST, and RefGene UCSC data sets set for an existing genome in IGB QuickLoad