[Bioperl-l] Emboss factory script

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


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


Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at accelrys.com
Accelrys (SciTegic R&D)             mobile: +1 858 205 3653
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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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