System Requirements =================== Samtools and HTSlib depend on the zlib library . 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 , 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.