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Command-line utilities you'll need
- faToTwoBit from UCSC (needed if there is no 2Bit file available)
- twoBitInfo from UCSC (needed to generate the genome.txt file)`faToTwoBit` 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)
- A version of `git` for your platform.
- IGBQuickLoad scripts in genomeshttps:/pub/src subversion repo.
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- bitbucket.org/lorainelab/genomesource (clone a copy locally using `git`)
Get the compiled programs these from UCSC and place in a directory in your PATH. Make sure they are executable in your PATH. 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.
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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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