System Requirements
===================
-Most of SAMtools functionality only depends on zlib which is included in
-this source code package. Compiling the alignment viewer further
-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 modifying two lines in Makefile
-as is described in the Makefile.
+SAMtools depends on the zlib library <http://www.zlib.net>. Version 1.2.3+ is
+preferred and with 1.2.3+ you can compile razip and use it to compress a FASTA
+file. SAMtools' faidx is able to index a razip-compressed FASTA file to save
+diskspace. Older zlib also works with SAMtools, but razip cannot be compiled.
+
+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='.
Compilation
===========
-Type `make' to compile samtools.
+Type `make' to compile samtools. If you have zlib >= 1.2.2.1, you can compile
+razip with `make razip'.
Installation
============
-Simply copy `samtools' and other executables/scripts in `misc' to a
-location you want (e.g. a directory in your $PATH). No further
-configurations are required.
+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.
projects / samtools.git / blobdiff