Samtools installation problem under Cygwin

[fbhe]

Hello,

I appreciate any help to resolve this issue. I got an error when I compiled Samtools under Cygwin 1.7 (windows vista 32 bit).
I had the following message:

$ make
make[1]: Entering directory `/home/fbhe/samtools-0.1.18'
make[2]: Entering directory `/home/fbhe/samtools-0.1.18'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/home/fbhe/samtools-0.1.18'
make[2]: Entering directory `/home/fbhe/samtools-0.1.18/bcftools'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/home/fbhe/samtools-0.1.18/bcftools'
make[2]: Entering directory `/home/fbhe/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/home/fbhe/samtools-0.1.18/misc'
gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmd up.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf. o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lm -lz
/usr/lib/gcc/i686-pc-cygwin/4.5.3/../../../../i686-pc-cygwin/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
Makefile:44: recipe for target `samtools' failed
make[1]: *** [samtools] Error 1
make[1]: Leaving directory `/home/fbhe/samtools-0.1.18'
Makefile:24: recipe for target `all-recur' failed
make: *** [all-recur] Error 1


Thanks,

fbhe

[mitochy]

I think it can't find zlib.
Maybe this will help:
this (they said to modify makefile and also install the lib)

http://gammon.com.au/forum/?id=9319

and this

http://cygwin.com/ml/cygwin-announce/2010-08/msg00000.html

[SeqVicious]

I'm also having a problem installing samtools under cygwin. after executing: tar xjvf <file location> I get the error of "Compressed file ends unexpectedly." It then proceeds to tell me that the file may be corrupted.

[SeqVicious]

Also, I have redownloaded and the same message shows up.

[Richard Finney]

Worked for me ... from cygwin ...

$ tar xjvf samtools-0.1.18.tar.bz2
samtools-0.1.18/
samtools-0.1.18/AUTHORS
samtools-0.1.18/COPYING
samtools-0.1.18/ChangeLog
samtools-0.1.18/INSTALL
samtools-0.1.18/Makefile
samtools-0.1.18/Makefile.mingw
samtools-0.1.18/NEWS
samtools-0.1.18/bam.c
samtools-0.1.18/bam.h

Either your tar is broken or your file is broken.
Try using "bzip2" -d to un-bzip2 it first
then "tar xvf" separately. This should tell you which is broken.


....

[emma924]

help

hello,did you resovled your problem? I have the same trouble with you, could you help me?

[Richard Finney]

emma924, you need to be more specific.

What version of gcc and cygwin do you have?
What version of samtools do you have?
What is your command line?
What are the results of this command?

[nuseqr]

Hi,

I need some help to resolve a similar problem. I got an error when I compiled Samtools under Cygwin (windows 8 64 bit).

I got the 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 from 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 for 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 for 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 for target 'all-recur' failed
make: *** [all-recur] Error 1

Thanks,

neseqr

[GenoMax]

Hi,

I need some help to resolve a similar problem. I got an error when I compiled Samtools under Cygwin (windows 8 64 bit).


bgzf.h:33:18: fatal error: zlib.h: No such file or directory
#include <zlib.h>
^
compilation terminated.
Makefile:56: recipe for 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 for 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 for target 'all-recur' failed
make: *** [all-recur] Error 1

Thanks,

neseqr

You need to install "zlib". Since this is windows you can find the compiled DLL here: http://zlib.net/zlib128-dll.zip. Once you download see the "usage.txt" files for instructions.

[nuseqr]

You need to install "zlib". Since this is windows you can find the compiled DLL here: http://zlib.net/zlib128-dll.zip. Once you download see the "usage.txt" files for instructions.

Thanks GenoMax,

Please see this note given in the usage.txt file

Using ZLIB1.DLL with gcc/Cygwin
===============================
ZLIB1.DLL is not designed to work with Cygwin. The Cygwin
system has its own DLL build of zlib, named CYGZ.DLL.

Does this mean that I need to add CYGZ.DLL?


I tried installing all zlib packages from a mirrors site, and got the following error message:

{$ 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 '
make[2]: Nothing to be done for 'lib'.
make[2]: Leaving 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 /bcftools'
make[2]: Nothing to be done for 'lib'.
make[2]: Leaving directory '/cygdrive/c/Users/ADMIN/Cygwin/home/samtools-0.1.19/ bcftools'
make[2]: Entering directory '/cygdrive/c/Users/ADMIN/Cygwin/home/samtools-0.1.19 /misc'
make[2]: Nothing to be done for 'lib'.
make[2]: Leaving directory '/cygdrive/c/Users/ADMIN/Cygwin/home/samtools-0.1.19/ misc'
gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_ rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_ind el.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamsh uf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lcurses - lm -lz -lpthread
errmod.o: In function `cal_coef':
/cygdrive/c/Users/ADMIN/Cygwin/home/samtools-0.1.19/errmod.c:44: undefined refer ence to `expl'
/cygdrive/c/Users/ADMIN/Cygwin/home/samtools-0.1.19/errmod.c:44.text+0xc0c): r elocation truncated to fit: R_X86_64_PC32 against undefined symbol `expl'
/cygdrive/c/Users/ADMIN/Cygwin/home/samtools-0.1.19/errmod.c:45: undefined refer ence to `logl'
/cygdrive/c/Users/ADMIN/Cygwin/home/samtools-0.1.19/errmod.c:45.text+0xc2d): r elocation truncated to fit: R_X86_64_PC32 against undefined symbol `logl'
collect2: error: ld returned 1 exit status
Makefile:47: recipe for target 'samtools' failed
make[1]: *** [samtools] Error 1
make[1]: Leaving directory '/cygdrive/c/Users/ADMIN/Cygwin/home/samtools-0.1.19'
Makefile:27: recipe for target 'all-recur' failed
make: *** [all-recur] Error 1}

[Jorge Amigo]

I never came across the need of installing samtools on Windows until very recently, and I stumbled upon this same issue. this previous thread had all the information I needed. I finally solved it by installing the same dependencies bedtools has (make, gcc-g++, zlib-devel) and by modifying the CFLAGS and DFLAGS lines of the Makefile file with these ones:

CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
CFLAGS= -I/usr/include/ncurses
DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log

[nuseqr]

Thanks Jorge Amigo,

I installed the zlib and lib packages from the mirror sites, and noticed that all mirror sites may not have all the packages. i did not modifying the CFLAGS and DFLAGS lines of the Makefile file.

and this is the following message got:

$ cd samtools-0.1.19
$ make
make: 'install' is up to date.


There were no error messages . Does this mean that samtools is installed and ready to use?? Do I still need to modifying the CFLAGS and DFLAGS lines of the Makefile file?

[Jorge Amigo]

if you didn't get any error messages you could try testing the command "./samtools.exe" inside that samtools-0.1.19 folder. if it returns the usage message, then you have successfully compiled samtools and generated a samtools.exe binary, which you can move around and place it wherever it best fits your needs.

[nuseqr]

I tried testing the command "./samtools.exe" inside that samtools-0.1.19

ADMIN@USER ~/samtools-0.1.19
$ ./samtools.exe
-bash: ./samtools.exe: No such file or directory

ADMIN@USER ~/samtools-0.1.19
$ ./samtools-0.1.19.exe
-bash: ./samtools-0.1.19.exe: No such file or directory

Tried again

ADMIN@USER ~/samtools-0.1.19
$ make
make: 'install' is up to date.

[GenoMax]

Can you post a listing of the files in the samtools directory?

$ ls -l samtools*