Question: Error In Samtool Installation Through Cygwin
0
gravatar for Nasrin
7.0 years ago by
Nasrin30
Nasrin30 wrote:

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.

samtools • 5.5k views
ADD COMMENTlink modified 7.0 years ago by Matt Shirley9.1k • written 7.0 years ago by Nasrin30

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.

ADD REPLYlink written 7.0 years ago by Djie180

but exe files do not execute in win32 !

ADD REPLYlink written 7.0 years ago by Nasrin30
1

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

ADD REPLYlink written 7.0 years ago by xied7520
0
gravatar for Matt Shirley
7.0 years ago by
Matt Shirley9.1k
Cambridge, MA
Matt Shirley9.1k wrote:

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.

ADD COMMENTlink written 7.0 years ago by Matt Shirley9.1k

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

ADD REPLYlink written 7.0 years ago by Nasrin30
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