PASTIS: Poisson-based Algorithm for STable Inference of DNA Structure

Dependencies

For Pastis:

• python (>= 2.7)
• numpy
• scipy
• scikit-learn
• pandas
• iced

Additional dependencies for new features (diploid inference multiscale optimization, etc):

• python (>= 3.6)
• autograd (>= 1.3)

Most of these dependencies can be installed at once using conda: http://conda.pydata.org/miniconda.html <http://conda.pydata.org/miniconda.html>_

Once conda is installed, just type the following::

conda install numpy scipy scikit-learn pandas

Or, to include the new features::

conda install numpy scipy scikit-learn pandas autograd

iced can be installed via::

pip install iced

Install PASTIS

This package uses distutils, which is the default way of installing python modules.

To install in your home directory, use::

python setup.py install --user

or using pip::

pip install --user pastis

To install for all users on Unix/Linux::

python setup.py build
sudo python setup.py install

or using pip::

pip install pastis

This will install a python package pastis, and five programs: pastis-mds, pastis-nmds, pastis-pm1, pastis-pm2, and pastis-poisson. Calling any of those five programs will display the help.