Metadata-Version: 1.1
Name: msprime
Version: 0.1.7
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 fresh Ubuntu 15.10 installation, do the
        following::
        
            $ sudo apt-get install pkg-config python-dev python-pip libgsl0-dev hdf5-tools 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
        
        See below for installation instructions for Macs.
        
        *************
        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
        
        To install the dependencies on OS X, we can use `Homebrew <http://brew.sh/>`_::
        
            $ brew update
            $ brew install gsl homebrew/science/hdf5
        
        ************
        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.
        
        ++++
        OS X
        ++++
        
        First, ensure that Homebrew is installed and up-to-date::
        
            $ brew update
        
        We need to ensure that the version of Python we used is installed via Homebrew
        (there can be issues with linking to HDF5 if we use the built-in version of
        Python or a version from Anaconda). Therefore, we install Python 3 using
        homebrew::
        
            $ brew install python3
            $ pip3 install --upgrade pip setuptools
        
        The previous step can be skipped if you wish to use your own Python installation,
        and already have a working pip.
        
        Now install the dependencies and msprime::
        
            $ brew install gsl homebrew/science/hdf5
            $ pip3 install msprime
        
        Check if it works::
        
            $ mspms 10 1 -T
        
        ****************
        Tested platforms
        ****************
        
        Msprime is highly portable, and has been successfully built and tested
        on the following platforms:
        
        ====================    ========        ======          ===========
        Operating system        Platform        Python          Compiler
        ====================    ========        ======          ===========
        Debian jessie           x86-64          2.7.9           gcc 4.9.2
        Debian jessie           x86-64          3.4.2           gcc 4.9.2
        Debian wheezy           i686            2.7.3           gcc 4.7.2
        Fedora 20               x86-64          2.7.5           gcc 4.8.3
        FreeBSD 10              x86-64          2.7.6           clang 3.4.1
        SunOS 5.10              SPARC           3.4.1           gcc 3.4.3
        OS X 10.10.5            x86-64          3.4.2           clang 7.0.0
        ====================    ========        ======          ===========
        
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
