Hi Chris, you can compile SamTools in Cygwin and it will create working Windows executables. The steps are described here: http://azaleasays.com/2014/09/29/install-samtools-in-cygwin/
The only problem is that you have to manually modify Makefile but this is somehow a traditional problem of SamTools (e.g., I cannot compile it on OpenSuSE without manual modifications of Makefile, too). Best regards Karel 2015-11-11 21:44 GMT+01:00 Christopher Wozniak < [email protected]>: > Hello, > I am having trouble compiling SamTools 1.2 on a Windows 8 machine. I am > new to SamTools and C compiling. I am using MinGW-w64 for compiling the > program. Every time the compiler stops: > > >mingw32-make > gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE > -D_CURSES_LIB=1 -I. -Ihtslib-1.2.1 -c -o bam_index.o bam_index.c > gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE > -D_CURSES_LIB=1 -I. -Ihtslib-1.2.1 -c -o bam_plcmd.o bam_plcmd.c > gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE > -D_CURSES_LIB=1 -I. -Ihtslib-1.2.1 -c -o sam_view.o sam_view.c > gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE > -D_CURSES_LIB=1 -I. -Ihtslib-1.2.1 -c -o bam_cat.o bam_cat.c > gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE > -D_CURSES_LIB=1 -I. -Ihtslib-1.2.1 -c -o bam_md.o bam_md.c > gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE > -D_CURSES_LIB=1 -I. -Ihtslib-1.2.1 -c -o bam_reheader.o bam_reheader.c > bam_reheader.c: In function 'bam_reheader': > bam_reheader.c:36:19: warning: variable 'old' set but not used > [-Wunused-but-set-variable] > bam_header_t *old; > ^ > gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE > -D_CURSES_LIB=1 -I. -Ihtslib-1.2.1 -c -o bam_sort.o bam_sort.c > bam_sort.c:32:19: fatal error: regex.h: No such file or directory > compilation terminated. > makefile:116: recipe for target 'bam_sort.o' failed > mingw32-make: *** [bam_sort.o] Error 1 > > I also tried Visual Studio and installing pcre. > > Sincerely, > Chris Wozniak > Post doc > University of Utah > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help > >
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