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Command-line utilities you'll need

• `faToTwoBit` faToTwoBit and `twoBitInfo scripts` 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)
• A version of `git` git for your platform.
• A version of subversion (svn) for your platform.
• IGBQuickLoad scripts in https://bitbucket.org/lorainelab/genomesource (clone a copy locally using `git`details on how to get the code are in the next sections)

Get the compiled programs from UCSC and place in a directory in your PATH. Make make sure they are executable on your system. Also make sure that the IGBQuickload scripts are in your PATH and that the cloned repository is added to your PYTHONPATH environment variable. (You may need to create it if it does not already exist 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.

Also, create a directory called `src` (for source code) and clone the IGBQuickload repository there.

export PATH=.:$HOME/bin:$HOME/src/genomesource:$PATH
export PYTHONPATH=$HOME/src/genomesource 

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
 co https://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:

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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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:

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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