[Bioperl-l] Bioperl problem

[chirag matkar]

Hello,


I am getting an Exception while running this script on Windows XP.

 -------------------------'align' is not recognized as an internal or
external co
mmand,
operable program or batch file.

------------- EXCEPTION -------------
MSG: ClustalW call ( align  -infile=seq.txt -output=gcg   -matrix=BLOSUM
-ktuple
=3 -outfile=C:\DOCUME~1\chirag\LOCALS~1\Temp\rIC8w2_4Ag\5JCfhbka_j 2>&1)
crashed
: 256
STACK Bio::Tools::Run::Alignment::Clustalw::_run
C:/Perl/lib/Bio/Tools/Run/Align
ment/Clustalw.pm:767
STACK Bio::Tools::Run::Alignment::Clustalw::align
C:/Perl/lib/Bio/Tools/Run/Alig
nment/Clustalw.pm:515
STACK toplevel C:\PROGRA~1\LUCKAS~1\ENGINS~1\data\CLUSTA~1.PL:33
-------------------------------------

Also the -outfile is taking any path which is not specified by me.is it
because of this?

On Tue, Jan 25, 2011 at 5:14 AM, Jun Yin <jun.yin at ucd.ie> wrote:

> Hi,
>
> I haven't run the code, but I spotted a few problems in the code.
>
> Yusheng, can you try to set the environment as
>
> BEGIN { $ENV{CLUSTALDIR} = "c:/work/ClustalW2 "};
> Instead of
> BEGIN { $ENV{CLUSTALDIR} = "c:/work/ClustalW2/clustalw2.exe"};
>
> If that still doesn't work, try to rename your clustalw2.exe into clustalw
> as well.
>
> Or, you can run your clustalw2 using system command, and read  in the
> alignment using Bio::AlignIO.
>
> Cheers,
> Jun Yin
> Ph.D. student in U.C.D.
>
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Monday, January 24, 2011 6:30 PM
> To: hanbobio
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Bioperl problem
>
> It's possible this is being caused by UNIX-specific issues with the method
> call (note the output redirection).  The problem is, I can't debug this
> myself w/o a Windows box to work off of.  Anyone Windows-savvy who can
> help?
>
> chris
>
> On Jan 22, 2011, at 4:28 AM, hanbobio wrote:
>
> > Hi,all
> >  When I run the Bioperl script on Windows XP, there are some problem.
> > I think the cause relate to the Bioperl tools. But I don't know how to
> dissove the problem.
> >  So I come here forhelp.
> > The problem is as the attached file
> > I had download the ClustalW2.exe, and the program is on
> C:/work/ClustalW2/clustalw2.exe. And the program worked when I used it
> directly. But it didn't work when I run the perl script(the attached
> file:test-new.pl). And I had installed the Bio-Run in the perl package
> management.
> >
> > Operation system: windows XP
> > Bioperl version: 1.6.0
> >
> >  Best regards!
> > yusheng liao<BioPerl
> Problem.doc><test-new.pl>_______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
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-- 
Regards,
Chirag Matkar