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  • Compile samtools on Windows so it doesn't need Cygwin

    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.

    Code:
    $ 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
    Our software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALi

  • #2
    Have you try this one?

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

    Comment


    • #3
      I am asking if samtools work on windows and C program or another software ?

      Comment


      • #4
        #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.
        Last edited by Richard Finney; 04-05-2016, 05:42 AM.

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