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README
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README
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_ _ _
_ __ ___ __ _| | _____ | | __ _| |_ ___ _ __
| '_ \ / _ \/ _` | |/ / _ \| |/ _` | __/ _ \| '__|
| |_) | __/ (_| | < (_) | | (_| | || (_) | |
| .__/ \___|\__,_|_|\_\___/|_|\__,_|\__\___/|_|
|_|
Copyright (C) 2010 by Daniel Jones <dcjones@cs.washington.edu>
All rights reserved.
This software should not be redistributed or used for any commercial
purpose without written permission from the author.
This software is provided ``AS IS'' and any express or implied
warranties, including, but not limited to, the implied warranties of
merchantability and fitness for a particular purpose, are disclaimed.
In no event shall the authors or the University of Washington be
liable for any direct, indirect, incidental, special, exemplary, or
consequential damages (including, but not limited to, procurement of
substitute goods or services; loss of use, data, or profits; or
business interruption) however caused and on any theory of liability,
whether in contract, strict liability, or tort (including negligence
or otherwise) arising in any way out of the use of this software, even
if advised of the possibility of such damage.
Installation Intructions
------------------------
Make sure you have the prerequisites listed below installed. Then,
./configure && make install
Prerequisites
-------------
Python (>=2.6) http://www.python.org/
Cython http://www.cython.org/
GSL http://www.gnu.org/software/gsl/
NLopt http://ab-initio.mit.edu/wiki/index.php/NLopt
Usage
-----
The script 'peakolate' is responsible for performing the scan.
Run, 'peakolate --help' for basic instructions.
the sequencing bias model can be trained with 'peakolate-seqbias'.