PyPop is a framework for processing genotype and allele data and running population genetic analyses.
- install developer command-line tools: https://developer.apple.com/downloads/ (includes
git,gcc) - Visit http://macports.org and follow the instructions there to install the latest version of MacPorts for your version of MacOS X.
- Set environment variables to use macports version of Python and other packages, packages add the following to
~/.bash_profile
export PATH=/opt/local/bin:$PATH
export LIBRARY_PATH=/opt/local/lib/:$LIBRARY_PATH
export CPATH=/opt/local/include:$CPATH
- Rerun your bash shell login in order to make these new exports active in your environment. At the command line type:
exec bash -login
git clone https://github.com/alexlancaster/pypop.git
Install the MacPorts packages
sudo port install swig-python gsl py27-numpy py-libxml2 py27-libxslt py-setuptools py27-pip
Set MacPorts to use the just-installed 2.7 MacPorts version of Python and pip:
sudo port select --set python python27
sudo port select --set pip pip27
Check that the MacPorts version of Python is active by typing: which python, if it is working correctly you should see the following:
/opt/local/bin/python
Need at least Fedora 25 for the appropriate dependencies:
sudo dnf install swig gsl-devel python2-numpy python-libxml2 libxslt-python python-setuptools python-pip
See DEV_NOTES.md for instructions on containerizing the install on a Centos/RHEL release.
Install the following packages
sudo apt install git libgsl-dev python-numpy python-libxml2 python-libxslt1 python-setuptools python-pip
The swig package in recent Ubuntu releases has bugs, you will need to compile the most recent from source, see also DEV_NOTES.md for details.
./setup.py build
These are examples of how to use PyPop. Specify the --help option to see an
explanation of the options available.
./bin/pypop.py -c tests/data/minimal.ini tests/data/USAFEL-UchiTelle-small.pop
This will generate the following two files, an XML output file and a plain text version:
USAFEL-UchiTelle-small-out.xml
USAFEL-UchiTelle-small-out.txt
./setup.py test
If you run into errors, file a bug (as per Support, below), include the output of py.test run in verbose mode and capturing the output
py.test -s -v
(See DEV_NOTES.md for more details on installing or running py.test outside the context of setuptools.)
Please submit bug reports and feature requests
https://github.com/alexlancaster/pypop/issues
When reporting bugs, especially during installation, please run the following and include the output:
echo $CPATH
echo $LIBRARY_PATH
echo $PATH
which python
If you are running on MacOS please also run and include the output of:
port installed
The code for PyPop is at
https://github.com/alexlancaster/pypop
PyPop is Copyright (C) 2003-2015. The Regents of the University of California (Regents)
PyPop is distributed under the terms of GPLv2