Cygwin - cannot execute binary file

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# 1  
Old 07-16-2012
Question Cygwin - cannot execute binary file

Hey all,

I am using Cygwin on a machine running windows 7 64bits. I am about to use the following command:
$ faToTwoBit in.fa out.2bit

In the manual on sourceforge it mentioned:
"Download blat and faToTwoBit and set the blat_bin and fatotwobit_bin entries in config.txt to the fully qualified paths of the blat and faToTwoBit binaries." Comrad 0.1.0 - fusioncomrad

I downloaded blat and faToTwoBit and put them in /Usr/bin
But when I try to run the command I see this error:
-bash: /usr/bin/faToTwoBit: cannot execute binary file

BTW, I checked the file that I downloaded and it is an ELF 64-bit LSB executable.
$ file /usr/bin/faToTwoBit
/usr/bin/faToTwoBit: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.9, stripped

Anyone can help me?! :|
# 2  
Old 07-16-2012
Cygwin is not Linux. Quoting Cygwin main page:

Cygwin is not a way to run native Linux apps on Windows. You must rebuild your application from source if you want it to run on Windows.
# 3  
Old 07-16-2012
Thanks jlliagre. What you're saying makes me worried! :\ And well.. it seems it's true! It's bin a while that I am using cygwin to run the unix commands and it worked perfectly so far! So, do you have any suggestion for this problem?

# 4  
Old 07-16-2012
As already suggested, recompile from source. In that specific case, that would be Comrad - Browse /0.1 at
# 5  
Old 07-16-2012
You need faToTwoBit compiled in Windows exe (PE) format but against cygwin1.dll not the native windows dll. You can't run native ELF binaries on Cygwin.

As fas as I know, the faToTwoBit application hasn't been ported yet to cygwin.

You can take a look here:

samtools installation - SEQanswers
SAMtools installation - SEQanswers

Seems to be problematic to compile under cygwin.
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