[Bioperl-l] Emboss factory script

Scott Markel SMarkel at accelrys.com
Tue Mar 10 13:15:27 EDT 2009


Shweta,

You should check the return value in line 6.  When we use BioPerl
to control EMBOSS programs we need to set some environment variables.
We set the following: EMBOSS_ROOT, EMBOSS_ACDROOT, EMBOSS_DB_DIR,
EMBOSS_DATA, and PATH.  Not all of the these are needed in every case.

Scott

Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at accelrys.com
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> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of shweta kagliwal
> Sent: Monday, 09 March 2009 11:57 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] Emboss factory script
> 
> I want to use Emboss programs.
> I tried running the attached script.
> But I get a warning:
> 
> Msg: Application [water] is not available.
> can't call method "run" on an undefined value at bpe.pl line 15.
> 
> I am not able to understand the problem. I just want to make pairwise
> alignments using emboss programs 'water' and 'needle' programatically.
> Please help me.
> Thanks.



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