INSTALL

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

Samtools and HTSlib depend on the zlib library <http://zlib.net>.  Building
them requires zlib development files to be installed on the build machine;
you may need to ensure a package such as zlib1g-dev (on Debian or Ubuntu Linux)
or zlib-devel (on RPM/yum-based distributions) is installed.

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 -lncurses. This can be set in Makefile by setting LIBCURSES= -lcurses vs
-lncurses.


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

'cd' to the samtools-1.x directory containing the package's source and type
'make' to compile samtools.

This samtools release contains a copy of HTSlib which will be used to build
samtools.  If you already have a system-installed HTSlib or another HTSlib
that you would prefer to build against, you can arrange this by overriding
$(HTSDIR) by typing 'make HTSDIR=/path/to/htslib-source' -- see the makefile
for details.


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

Type 'make install' to install the samtools executable and various scripts
and executables from misc/ and a manual page to /usr/local.

Type 'make prefix=/path/to/dir install' to install everything under your
choice of installation directory.  The install target also understands
DESTDIR and the other usual installation directory variables.

The bgzip and tabix utilities are provided by HTSlib.  If you have not also
installed HTSlib separately, you may wish to install these utilities by hand
by copying samtools-1.x/htslib-1.x/{bgzip,tabix} to the same bin directory
to which you have installed samtools et al.