[Samtools-help] problem compiling on a linux server

[Ryan M. <rm...@bc...>]

I am unable to compile the current SVN checkout of SAMtools on our 64-bit linux (CentOS) server.  I first tried to compile with the default Makefile but the lack of a system-wide install of zlib resulted in an early compile failure.  As suggested, I tried using Makefile.lite but also did not succeed.  Here is the result:

make -f Makefile.lite 
make[1]: Entering directory `/home/rmorin/samtools'
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  bam.c -o bam.o
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  bam_import.c -o bam_import.o
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  bam_pileup.c -o bam_pileup.o
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  bam_lpileup.c -o bam_lpileup.o
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  bam_sort.c -o bam_sort.o
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  bam_index.c -o bam_index.o
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  bgzf.c -o bgzf.o
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  faidx.c -o faidx.o
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  bam_tview.c -o bam_tview.o
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  bam_maqcns.c -o bam_maqcns.o
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  bam_aux.c -o bam_aux.o
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  bam_plcmd.c -o bam_plcmd.o
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  bam_mate.c -o bam_mate.o
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  bam_rmdup.c -o bam_rmdup.o
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  glf.c -o glf.o
ar -cru libbam.a bam.o bam_import.o bam_pileup.o bam_lpileup.o bam_sort.o bam_index.o bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o bam_mate.o bam_rmdup.o glf.o
gcc -c -g -Wall -O2 -m64  -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF  bamtk.c -o bamtk.o
gcc -g -Wall -O2 -m64  -o samtools bamtk.o -lm -lz -L. -lbam
bamtk.o(.text+0x436): In function `main':
/home/rmorin/samtools/bamtk.c:116: undefined reference to `bam_flagstat'
collect2: ld returned 1 exit status
make[1]: *** [samtools] Error 1
make[1]: Leaving directory `/home/rmorin/samtools'
make: *** [all-recur] Error 1

Is there a way I can get around this?  I would prefer to install using zlib features for obvious reasons.  I have limited experience with makefiles, so I don't know how/whether I can adjust the makefile to point to my personal installation of zlib.  I tried adding the path to the INCLUDES line in the Makefile but this also failed.  Any guidance would be greatly appreciated.

Thanks,

Ryan