INSTALL

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

SAMtools depends on the zlib library <http://www.zlib.net>. Version 1.2.3+ is
preferred.

SAMtools' faidx is able to index a bgzip-compressed FASTA file to save
diskspace.

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 changing:
`-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and
comment out the line starting with `LIBCURSES='.
Note that on some systems the library is available as -lcurses while on others
as -lnurses. This can be set in Makefile by setting LIBCURSES= -lcurses vs
-lncurses.


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

Type `make' to compile samtools.


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

Copy `samtools', `bcftools/bcftools' and other executables/scripts in `misc' to
a location you want (e.g. a directory in your $PATH). You may also copy
`samtools.1' and `bcftools/bcftools.1' to a directory in your $MANPATH such
that the `man' command may find the manual.