Merge branch 'vsbuffalo-master' into develop

[samtools.git] / INSTALL

diff --git a/INSTALL b/INSTALL
index faa3eaf10d66354329abd106c4f27d4230f8756c..37d84a9e48b3247f8b807d7d983e182e17bb1204 100644 (file)
--- a/INSTALL
+++ b/INSTALL
@@ -1,8 +1,30 @@
-Compiling samtools requires the zlib library <http://www.zlib.net/>;
-compiling the alignment viewer further requires the GNU ncurses library
-<http://www.gnu.org/software/ncurses/>.
-
-Please type `./configure; make' to compile samtools. If it fails, try
-`make -f Makefile.generic'. If the compilation still fails due to errors
-in RAZF or the lack of ncurses, try `make -f Makefile.lite' to disable
-the alignment viewer and the RAZF-enhanced FASTA indexer.
+System Requirements
+===================
+
+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. If you have zlib >= 1.2.2.1, you can compile
+razip with `make razip'.
+
+
+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.