Compile samtools on Windows so it doesn't need Cygwin

[imilne]

I assume this can be done, because the binaries that are available on the samtools website (for 0.1.7 and earlier) don't need a Cygwin environment to run?

I can compile everything fine within Cygwin, but attempting to run the following with the latest source code (0.1.11) fails.

$ make -f Makefile.mingw
gcc.exe -c -g -Wall -O2 -mno-cygwin -D_CURSES_LIB=2 -D_USE_KNETFILE -Iwin32 bam_tview.c -o bam_tview.o
gcc.exe -c -g -Wall -O2 -mno-cygwin -D_CURSES_LIB=2 -D_USE_KNETFILE -Iwin32 bam_maqcns.c -o bam_maqcns.o
bam_maqcns.c: In function `ks_shuffle_uint32_t':
bam_maqcns.c:8: warning: implicit declaration of function `drand48'
gcc.exe -c -g -Wall -O2 -mno-cygwin -D_CURSES_LIB=2 -D_USE_KNETFILE -Iwin32 bam_plcmd.c -o bam_plcmd.o
bam_plcmd.c: In function `pileup_func':
bam_plcmd.c:247: warning: implicit declaration of function `drand48'
In file included from bam2bcf.h:6,
                 from bam_plcmd.c:526:
bcftools/bcf.h:35:18: bgzf.h: No such file or directory
make: *** [bam_plcmd.o] Error 1

Am I even using the right command?

I ultimately need a samtools.exe that can be given to people that don't have Cygwin.

Thanks

[vixensjlin]

Have you try this one?

samtools (Tools for alignments in the SAM format) on BOW - Bioinformatics On Windows

[esraa]

I am asking if samtools work on windows and C program or another software ?

[Richard Finney]

#1 Install bzip2 libraries on cygwin.

#2 several ways around drand48() problem.

You can duckduckgo for "cygwin drand48"
suggestion but I have not tried:
One solution is just doing this ... just jam it in a header file.

#ifdef CYGWIN32
#define rand48 random
#endif

You can hack the makefile on the compiler options line to put in this define.

You can also swiped drand48.c from somewhere and just jam it in a C file.

I've compiled samtools on cygwin using gcc, though it's a moving target as it's fine tuned for Linux and
portability to windows was never a high priority. Code changes don't always port easily.

Compiling with Visual C is an epic adventure.