How to compile and work samtools with cygwin -


i need resolve problem. got error when compiled samtools under cygwin (windows 8 64 bit).

i got following message:

admin@user ~/samtools-0.1.19

$ make     make[1]: entering directory '/cygdrive/c/users/admin/cygwin/home/samtools-0.1.19'     make[2]: entering directory '/cygdrive/c/users/admin/cygwin/home/samtools-0.1.19'     gcc -c -g -wall -o2 -d_file_offset_bits=64 -d_largefile64_source -d_use_knetfile -d_curses_lib=1 -dbgzf_cache -i. bgzf.c -o bgzf.o     in file included bgzf.c:32:0:     bgzf.h:33:18: fatal error: zlib.h: no such file or directory     #include <zlib.h>         ^          compilation terminated.     makefile:56: recipe target 'bgzf.o' failed     make[2]: *** [bgzf.o] error 1 make[2]: leaving directory '/cygdrive/c/users/admin/cygwin/home/samtools-0.1.19' makefile:27: recipe target 'lib-recur' failed make[1]: *** [lib-recur] error 1 make[1]: leaving directory '/cygdrive/c/users/admin/cygwin/home/samtools-0.1.19' makefile:27: recipe target 'all-recur' failed make: *** [all-recur] error 1

please tell me went wrong , how need correct it. tried make few changes makefile changed -d_curses_lib=1 -d_curses_lib=0 changed "libcurses= -lcurses # -lxcurses" "libcurses= # -lcurses # -lxcurse

the error message still continues, please help..

i had same issue, , solved following steps:

start cygwin installer, in "select package" page, search , install gcc-g++, gdb, make, libncurses, zlib, zlib-devel.

download , extract samtools.

append -dexpl=exp -dlogl=log 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 clean previous build attempts.

then run make.

copy samtools.exe , misc folder system path. or samtools version 1.0 or later, run make install.

please note: samtools in version 1.1. should try first.

more information on my blog.


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