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INSTALL.rst

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Plastid installation

Requirements

Non-python

Compiling plastid requires a standard C build system (e.g. GCC or clang, plus the standard C library, and linking tools) as well as zlib. The good news is that these are already required by plastid's dependencies, such as numpy and pysam, so you probably already have them.

Python

Plastid requires Python 2.7 or 3.3 or greater, as well as a number of Python packages. All but three of these (numpy, pysam, and Cython) -- will be automatically handled by Python's package management systems (pip or easy_install if you are using them). numpy, pysam and Cython are required for plastid's setup script to run.

Compiling & installing

  1. First, make sure you have GCC or clang, zlib and its headers, and the Python headers. On an Ubuntu system, you could get these by typing:

    $ sudo apt-get install build-essential zlib1g zlib1g-dev python-dev

  2. Install numpy, pysam, and Cython:

    $ sudo pip install numpy pysam cython

    or, for a single user install:

    $ pip install --user numpy pysam cython

  3. Compile & install plastid:

    $ python setup.py build
$ sudo python setup.py install

    or, for a single user install:

    $ python setup.py build
$ python setup.py install --user

Building the documentation

Building the documentation requires plastid to be compiled so that its Cython extensions are importable. In addition, sphinx, sphinxcontrib-bibtex, sphinxcontrib-argdoc, and numpydoc are required. Install these:

$ sudo pip install sphinx sphinxcontrib-bibtex sphinxcontrib-argdoc numpydoc

Then make the documentation:

$ cd docs
$ make html

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