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

pIRS requires the zlib library (http://www.zlib.net/) to be installed.

The Boost library is no longer needed by pIRS.

To compile, run the commands:

	$ ./configure
	$ make
	$ make install

In addition, the `configure' script recognizes the following options:
	
--prefix=PREFIX
	Set installation root.  e.g. if you use --prefix=/usr, we install pirs
	to /usr/bin/pirs, and the profiles to /usr/share/pirs.  pIRS must be
	able to find its profiles in order to simulate reads, unless you run
	with `--no-subst-errors --no-gc-bias --no-indel-errors' to disable all
	the bias (not recommended).

--disable-threads
	Build single-threaded program.

--disable-sse2
	Use the generic Mersenne twister random number generator algorithm
	rather than the SSE2-accelerated version.

--disable-pirs-simulate
	Only support the `pirs diploid' command.

--disable-pirs-diploid
	Only support the `pirs simulate' command.
