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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)
- 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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Get the QuickLoad data repo
Check out or update a copy of IGB QuickLoad data
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directories.
Open a terminal (UNIX shell) and change into the directory where you want your checked-out copy of the genomes repository to reside.
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Questions about using subversion? See: Version Control with Subversion.
Check out or update a copy of IGB QuickLoad source code (src) directory.
As before, open a terminal and change into the directory where you want your checked-out copy of the genomes src code to reside. A good place for checked-out code is a directory named src in your home directory.
To set up a src directory for checked-out code:
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cd
mkdir src
cd src
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Then, use svn to get a copy of the QuickLoad source code from the repo and save it to a directory named quickload_src:
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$ svn co https://svn.transvar.org/repos/genomes/trunk/pub/src quickload_src
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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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export PATH=$HOME/src/quickload_src:$PATH
export PYTHONPATH=$HOME/src/quickload_src:$PYTHONPATH
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Test that it worked by opening a new terminal and typing sample.py at the prompt. If your path is correctly configured, the script will run without error.
Get the data from UCSC
Open a Web browser and find the genome you would like to add in the Table Browser at UCSC
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