[Bioperl-l] clustalw.exe

Chris Fields cjfields at illinois.edu
Sun Aug 22 15:56:58 EDT 2010

On Aug 21, 2010, at 9:07 AM, keiko wrote:

> Katrin wrote:
>> hello, I am a new Perl/Bioperl-User and first I must excuse me for my
>> really bad english, but I hope everybody will understand me. I have the
>> following problem: In my Perl-skript is the following system call:
>> $y=exec("C:\\Programme\\xampp-win32-1.5.1\\xampp\\perl\\clustalw.exe
>> C:\\Programme\\xampp-win32-1.5.1\\xampp\\htdocs\\gene\\clustal.fasta"); If
>> I call this Script with the Shell (cmd.exe) everything works correctly.
>> But if I call this script with PHP I get the following error message:
>> Error: unknown option
>> /C:\Programme\xampp-win32-1.5.1\xampp\htdocs\gene\clustal.fasta. I tried
>> also system and qx. And I tested the environment variables: I wrote a
>> bat-file with the definition of all environment-variables and the system
>> call, but this did not work, too. The same problem is in php. The
>> PHP-Scipt is called from html and I worked under WindowsXP with xampp. I
>> hope, somebody can help me. greetings Katrin
> Hi. I also have a problem with this one. I want to call clustalw using php.
> Can I ask what you included in your bat-file and where did you download your
> clustal? thanks a lot!

Not sure, but what does this have to do with BioPerl?


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