INSTALL

System Requirements
===================

SAMtools depends on the zlib library <http://www.zlib.net>. The latest
version 1.2.3 is preferred and with the latest version you can compile
razip and use it to compress a FASTA file. SAMtools' faidx is able to
index a razip-compressed FASTA file to save diskspace. Older zlib also
works with SAMtools, but razip cannot be compiled.

The text-based viewer (tview) requires the GNU ncurses library
<http://www.gnu.org/software/ncurses/>, which comes with Mac OS X and
most of the modern Linux/Unix distributions. If you do not have this
library installed, you can still compile the rest of SAMtools by
manually modifying one line in Makefile.

Pysam requires Python (2.6 or greater) and Cython (0.22 or greater).
It has not been tested on many other platforms.

Compilation
===========

Unpack the distribution and enter the pysam directory. Type 

python setup.py build

to compile.

Installation
============

Type 

   python setup.py install

to install it within the site-packages directory of your python
distribution. Type

   python setup.py install --help 

for more options.

Build the documentation
=======================

Install a version of Sphinx that matches your Python version (2 or 3) and run

    python setup.py build_sphinx

or

    python3 setup.py build_sphinx

The documentation will be put into build/sphinx.

Architecture specific options
=============================

Pysam has been compiled on various Linux systems and works
with python 2.6 and python 2.5.

Python 2.7 and Python 3 have not been tested.

Windows support does not work yet.