[Bioperl-l] clustalw.exe

keiko i.hatethispart at ymail.com
Sat Aug 21 10:07:28 EDT 2010

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!
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