Error In Samtool Installation Through Cygwin

Question

[Nasrin]

I'm trying to install a samtool through cygwin on windows.I moved installation files to the folder with the makefile . when I try to make the files, it gives me this error:

$ make

make[1]: Entering directory `/home/Nasrin/samtool'

make[2]: Entering directory `/home/Nasrin/samtool'

gcc -c -g -Wall -O2 -DFILEOFFSETBITS=64 -DUSEKNETFILE -DCURSES_LIB=1 -I. bgzf.c -o bgzf.o

/usr/lib/gcc/i686-pc-cygwin/4.5.3/cc1.exe: error while loading shared libraries: cygz.dll: cannot open shared object file: No such file or directory

Makefile:20: recipe for target `bgzf.o' failed

make[2]: * [bgzf.o] Error 1 make[2]: Leaving directory `/home/Nasrin/samtool'

Makefile:23: recipe for target `lib-recur' failed

make[1]: * [lib-recur] Error 1

make[1]: Leaving directory `/home/Nasrin/samtool'

Makefile:23: recipe for target `all-recur' failed

make: * [all-recur] Error 1

thanks for any advice on this problem.

[Djie]

If installing through cygwin is not a specific requirement, you can try installing the windows port for samtools: http://bow.codeplex.com/. This is probably a lot easier.

[Nasrin]

but exe files do not execute in win32 !

[xied75]

Hi, Nasrin, that is correct it won't run under 32 bit windows. Because 32 bit OS limit the memory you can have thus making these tools less useful (especially for BWA etc.) Also today 64 bit is the default for Windows, even very cheap range laptop has 64 bit installation. So maybe you could consider using a 64 bit windows for your work?

Samtools under cygwin is very buggy, because that's another layer on top of Linux Glibc and Windows C runtime library.

Best,

dong

Answer 1

[Matt Shirley]

In your cygwin root filesystem there should be a copy of cygz.dll in /bin. If there is not, you have maybe one of two issues. First, the output of echo $PATH should include the /bin directory. If not, then read up on setting your user's $PATH environment variable. Otherwise, it looks like you might need to run the cygwin installer again and select "repair", or re-install the base system.

[Nasrin]

i have cygz.dll in cygwin root filesystem and i have installed and even downloaded cygwin with all its dependencies again!