Install samtools in Cygwin

Start the Cygwin Installer, in the “Select Package” page, search and install gcc-g++, gdb, make, libncurses, zlib, zlib-devel.

Download and extract samtools.

Append -Dexpl=exp -Dlogl=log to Makefile’s default DFLAGS line, such as:

DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log

Run make clean to clean up previous build attempts.

Then run make.

If it works, copy samtools.exe and misc folder to the system path. Or for samtools version 1.0 or later, run make install.

If it still does not work, change -D_CURSES_LIB=1 to -D_CURSES_LIB=0 in DFLAGS line, such as:

DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log

and comment out the line starting with LIBCURSES =. Then run make. This will compile samtools without the text-based viewer (tview).