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A fast and accurate coalescent simulator.

Project description

Msprime is a reimplementation of Hudson’s classical ms program for modern datasets. The Python API and storage format are currently under development and are not fully documented, but the command line interface mspms is reliable and ready for use. This program provides a fully ms compatible interface, and can be used as a drop-in replacement in existing workflows.

Requirements

Msprime requires Python 2.7+ (Python 3 versions are fully supported from 3.1 onwards), the GNU Scientific Library, and HDF5 version 1.8 or later. These packages are available for all major platforms. For example, to install on Debian/Ubuntu use:

# apt-get install python-dev libgsl0-dev libhdf5-serial-dev pkg-config

TODO

  • Need installation instructions for an RPM based distribution, HomeBrew/MacPorts and possibly a linux distro where we are missing root access.

FreeBSD 10.0

To install on FreeBSD, install the gsl and hdf5-18 packages as follows:

# pkg install gsl hdf5-18

TODO Finish installation instructions.

Installation

The simplest method of installation is to use PyPI and pip:

$ pip install msprime --user --pre

will install msprime your user Python installation. This should work in most cases (but see the Requirements section).

To use the ms-compatible command line program, you must ensure that the ~/.local/bin/ directory is in your PATH.

Project details


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Filename, size & hash SHA256 hash help File type Python version Upload date
msprime-0.1.1a5.tar.gz (65.9 kB) Copy SHA256 hash SHA256 Source None Jun 23, 2015

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