Shell Programming and Scripting

Hey all,

I am using Cygwin on a machine running windows 7 64bits. I am about to use the following command:

Code:

$ 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." SourceForge.net: 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:

Code:

-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.

Code:

$ 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?! :|
Tnx

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.

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?

Tnx

As already suggested, recompile from source. In that specific case, that would be Comrad - Browse /0.1 at SourceForge.net

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.