README

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=== Installation === 
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==== Dependencies ====
{{{
- nose (for nosetest)
- for spline alignment, one of the following two:
-- scikit-datasmooth
-- rpy2 and R installation
-- python-xlwt
}}}

==== Instructions ====
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To install you should run

$ python setup.py install 

if you would like to install it to a local folder, you can use 

$ python setup.py install --prefix=/your/install/path 

to install it to any path on your system (just make sure that this path is in
your $PYTHONPATH and add the./bin folder to your $PATH).

}}}

=== Extra packages ===

There are some extra packages that can increase the features and improve the speed of the toolset

==== Fast lowess ==== 
To get fast lowess performance (several orders of magnitude faster), do the
following

git clone https://github.com/carljv/Will_it_Python.git
cd Will_it_Python/MLFH/CH2/lowess\ work/
python setup.py build
sudo python setup.py install


}}}

=== Testing === 
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run all tests 

$ nosetests test

with coverage analysis

$ nosetests test --with-coverage --cover-package=msproteomicstoolslib

no slow tests

$ nosetests -a '!slow' test

}}}