INSTALL.txt

MashMap is normally distributed as a dependency-free binary for Linux or OSX). 
This source distribution is intended for other operating systems or for development. 
MashMap requires c++11 to build, which is available in and GCC >= 4.8 and 
OSX >= 10.7.

Dependencies:
-------------
   - Autoconf ( http://www.gnu.org/software/autoconf/ )
   - either...
       GNU Scientific Library ( http://www.gnu.org/software/gsl/ )
     or..
       Boost Library ( http://www.boost.org ) (see "-with-boost" below)
   - Zlib ( included with OS X and most Linuxes, http://www.zlib.net ) *


Steps:
------
   ./bootstrap.sh
   ./configure [--prefix=...] [--with-gsl=...] [--with-boost=...]
   make


Products:
---------
   - command line tool ( <prefix>/bin/mashmap)



Configure options:
------------------
--prefix=</path/to/install>
  Installs binaries to bin/ and libraries to lib/ within this path. The default
  is /usr/local/, which will typically require sudo for make install. Must be
  absolute path.
--with-gsl=</path/to/gsl/>
  Where to find the GNU Scientific library install if not in the default
  location (/usr/local). Must be absolute path and should not include bin/ or
  lib/.
--enable-static-gsl
  Statically link the GNU Scientific library instead of dynamically. Be mindful
  of licensure if distributing.
--with-boost=</path/to/boost/>
  Use Boost from this location, instead of GSL. Must be absolute path and should
  not include bin/ or lib/. Will be statically linked. Be mindful of licensure
  if distributing.
  
* If Zlib is not installed in a standard system location (it usually is),
  CXXFLAGS and LDFLAGS will have to be modified before making.