Basic Installation
==================

To build and install Samtools, 'cd' to the samtools-1.x directory containing
the package's source and type the following commands:

    ./configure
    make
    make install

The './configure' command checks your build environment and allows various
optional functionality to be enabled (see Configuration below).  If you
don't want to select any optional functionality, you may wish to omit
configure and just type 'make; make install' as for previous versions
of samtools.  However if the build fails you should run './configure'
as it can diagnose the common reasons for build failures.

The 'make' command builds samtools and various miscellaneous utilities.
If compilation fails you should run './configure' as it can diagnose
problems with your build environment that cause build failures.

(The bgzip, htsfile, and tabix utilities are provided by HTSlib.  If you are
not also compiling HTSlib separately, you may wish to compile these utilities
in the associated copy of HTSlib.  Type 'make all all-htslib' to do this.)

The 'make install' command installs the samtools executable and various
scripts and executables from misc/ and a manual page to /usr/local.
The installation location can be changed by configuring with --prefix=DIR
or via 'make prefix=DIR install' (see Installation Locations below).

(If you have not also installed HTSlib separately, you may wish to install
the bgzip, htsfile, and tabix utilities from the associated copy of HTSlib.
Type 'make install install-htslib' to do this.)

Typically you will want to enable HTSlib's HTTPS/etc plugin etc.
See README for recipes for typical installation.


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

Samtools requires the zlib library <http://zlib.net> and (optionally) a
curses or GNU ncurses library <http://www.gnu.org/software/ncurses/>.
If you are unsure about this, be sure to use './configure' to determine
whether you have these libraries and to help diagnose which packages may
need to be installed on your build machine to provide them.


Configuration
=============

By default, './configure' examines your build environment, searching for a
usable HTSlib and checking for requirements such as the curses development
files, and arranges for a plain samtools build.

This samtools release contains a copy of the HTSlib source code 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 via the --with-htslib option.

The following configure options can be used to enable various features and
specify further optional external requirements:

--with-htslib=DIR
    Specifies the HTSlib source tree or installation directory that samtools
    should use to parse bioinformatics file formats etc.  Configure will check
    that DIR appears to contain HTSlib source files or to be the root of an
    installation directory (i.e., it has 'include' and 'lib' subdirectories
    containing HTSlib headers and libraries).

    By default, configure looks for an HTSlib source tree within or alongside
    the samtools source directory; if there are several likely candidates,
    you will have to choose one via this option.

--with-htslib=system
    Ignores any nearby HTSlib source trees, and builds samtools using an
    existing HTSlib installation in a system directory (i.e., a directory
    already being searched by $CPPFLAGS/$LDFLAGS).

--without-curses
    Omit the curses-based 'tview' subcommand from the build.  If you do not
    have curses on your build machine or otherwise don't want the interactive
    tview subcommand, this option disables it and skips testing for working
    curses development files.

If you are building with an HTSlib source tree, HTSlib's configure script
will also be run.  So HTSlib configure options can also be used and will be
passed down to the HTSlib configure.  See HTSlib's INSTALL documentation for
details of these options.

The configure script also accepts the usual options and environment variables
for tuning installation locations and compilers: type './configure --help'
for details.  For example,

    ./configure CC=icc --prefix=/opt/icc-compiled

would specify that samtools is to be built with icc and installed into bin,
lib, etc subdirectories under /opt/icc-compiled.


Installation Locations
======================

By default, 'make install' installs samtools and the utilities under
/usr/local/bin and manual pages under /usr/local/share/man.

You can specify a different location to install Samtools by configuring
with --prefix=DIR or specify locations for particular parts of HTSlib by
configuring with --bindir=DIR and so on.  Type './configure --help' for
the full list of such install directory options.

Alternatively you can specify different locations at install time by
typing 'make prefix=DIR install' or 'make bindir=DIR install' and so on.
Consult the list of prefix/exec_prefix/etc variables near the top of the
Makefile for the full list of such variables that can be overridden.

You can also specify a staging area by typing 'make DESTDIR=DIR install',
possibly in conjunction with other --prefix or prefix=DIR settings.
For example,

    make DESTDIR=/tmp/staging prefix=/opt

would install into bin and share/man subdirectories under /tmp/staging/opt.
