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Update install.rst
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jaredgk committed Jan 12, 2021
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Installation
============

###########
From Source
###########

The most current version of the PPP can be installed by obtaining the source code from the PPP GitHub repository. This can be done with:

.. code-block:: bash
git clone https://github.com/jaredgk/PPP
It can then be installed with either of these two commands, after CDing into the created directory (first allows editing the source code, second installs from source):

.. code-block:: bash
pip install -e .
python setup.py install
#########
From PyPi
#########
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conda activate py-popgen
conda install -c jaredgk -c bioconda py-popgen
###########
From Source
###########

The most current version of the PPP can be installed by obtaining the source code from the PPP GitHub repository. This can be done with:

.. code-block:: bash
git clone https://github.com/jaredgk/PPP
It can then be installed with either of these two commands, after CDing into the created directory (first allows editing the source code, second installs from source):

.. code-block:: bash
pip install -e .
python setup.py install
###################
-------------------
Python Dependencies
###################
-------------------

The PPP requries a number of python libraries, including:
If installing PPP from source, multiple python and non-python dependencies must also be installed. The PPP requries a number of python libraries, including:

* `The SciPy Ecosystem <https://www.scipy.org/about.html>`_ (i.e. numpy, scipy, pandas, matplotlib, etc.)
* `Pysam <https://github.com/pysam-developers/pysam>`_
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