Metadata-Version: 1.1
Name: msprime
Version: 0.1.1
Summary: A fast and accurate coalescent simulator.
Home-page: http://pypi.python.org/pypi/msprime
Author: Jerome Kelleher
Author-email: jerome.kelleher@well.ox.ac.uk
License: GNU LGPLv3+
Description: =======
        msprime
        =======
        
        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.
        
        Msprime can simulate the coalescent with recombination much
        faster than programs based on the Sequentially Markov Coalescent
        for large sample sizes and has very reasonable memory requirements. Msprime
        makes it possible to simulate chromosome sized regions with hundreds of
        thousands of samples.
        
        Please see the `documentation <https://msprime.readthedocs.org/en/latest/>`_
        for further details.
        
        ***********
        Quick Start
        ***********
        
        To install and run ``msprime`` on a Ubuntu 14.10 installation do the
        following::
        
            $ sudo apt-get install python-dev libgsl0-dev libhdf5-serial-dev
            $ sudo pip install msprime
            $ mspms 2 1 -t 1
            /usr/local/bin/mspms 2 1 -t 1
            5338 8035 23205
        
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        If you do not wish to install ``msprime`` to your system, you can try
        it out in a `virtualenv <http://virtualenv.pypa.io/en/latest/>`_ as
        follows::
        
            $ virtualenv msprime-env
            $ source msprime-env/bin/activate
            (msprime-env) $ pip install msprime
            (msprime-env) $ mspms
        
        
        *************
        Requirements
        *************
        
        Msprime requires Python 2.7+ (Python 3 versions are fully supported from
        3.1 onwards), the `GNU Scientific Library <http://www.gnu.org/software/gsl/>`_,
        and `HDF5 <https://www.hdfgroup.org/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
        
        For Redhat/Fedora use::
        
            # yum install gsl-devel hdf5-devel
        
        On FreeBSD we can use ``pkg`` to install the requirements::
        
            # pkg install gsl hdf5-18
        
        ----
        TODO
        ----
        
        - Add instructions for HomeBrew/MacPorts.
        
        ************
        Installation
        ************
        
        The simplest method of installation is to use PyPI and pip::
        
            # pip install msprime
        
        This will work in most cases, once the `Requirements`_ have been
        satisfied. See below for platform specific build instructions when this
        fails.
        
        If you do not have root access to your machine, you can install
        ``msprime`` into your local Python installation as follows::
        
            $ pip install msprime --user
        
        To use the ``mspms`` program you must ensure
        that the ``~/.local/bin`` directory is in your ``PATH``, or
        simply run it using::
        
            $ ~/.local/bin/mspms
        
        To uninstall ``msprime``, simply run::
        
            $ pip uninstall msprime
        
        ------------------------------
        Platform specific installation
        ------------------------------
        
        This section contains instructions to build on platforms
        that require build time flags for GSL and HDF5.
        
        ++++++++++++
        FreeBSD 10.0
        ++++++++++++
        
        Install the prerequisitites, and build ``msprime`` as follows::
        
            # pkg install gsl hdf5-18
            # CFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib pip install msprime
        
        This assumes that root is logged in using a bash shell. For other shells,
        different methods are need to set the ``CFLAGS`` and ``LDFLAGS`` environment
        variables.
        
        ---
        OSX
        ---
        
        *TODO*
        
Keywords: Coalescent simulation,ms
Platform: POSIX
Classifier: Programming Language :: C
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.1
Classifier: Programming Language :: Python :: 3.2
Classifier: Programming Language :: Python :: 3.3
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Other Environment
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
Classifier: Operating System :: POSIX
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
