[Bioperl-l] problem with Bio::Tools::EMBOSS

[ANJAN PURKAYASTHA]

guys,
thanks! i got bioperl-run to work.
next question, let's say i want to run the palindrome program in emboss
using the bioperl wrapper.   now, palindrome takes in a list of parameter
values- these are fed into emboss as a key-value hash. where do i find the
correct names of the keys to create the input hash?
tia.

anjan

On Mon, Mar 3, 2008 at 2:25 PM, Mauricio Herrera Cuadra <
arareko at campus.iztacala.unam.mx> wrote:

> Hi Anjan,
>
> It looks like you are using the latest BioPerl developer release
> (bioperl-1.5.2_102) from CPAN, to have Bio::Factory::EMBOSS available
> then you should try installing the latest BioPerl-run as well
> (bioperl-run-1.5.2_100). After you install it, you'll have to modify
> your 'use lib' pragma for your script to work as you expect:
>
> use lib "/Users/anjan/perl_directory/bioperl-run-1.5.2_100/";
> use Bio::Factory::EMBOSS;
>
> Hope this helps.
>
> Regards,
> Mauricio.
>
>
> ANJAN PURKAYASTHA wrote:
> > hi
> > i am tried to use the perl wrappers for EMBOSS with:
> >
> > use lib "/Users/anjan/perl_directory/bioperl-1.5.2_102/";
> > use Bio::Factory::EMBOSS;
> >
> > however it seems that Bio::Factory::EMBOSS cannot be found in the
> bioperl
> > directory mentioned above.
> >
> > so i tried to install Bio::Factory::EMBOSS from the cpan website. i got
> the
> > attached error message.
> >
> > any ideas on what i need to do to  make this work?
> > all advice will be appreciated.
> >
> > tia,
> >
> > anjan
> >
> >
> >
> >
> > ------------------------------------------------------------------------
> >
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>
> --
> MAURICIO HERRERA CUADRA
> arareko at campus.iztacala.unam.mx
> Laboratorio de Genética
> Unidad de Morfofisiología y Función
> Facultad de Estudios Superiores Iztacala, UNAM
>
>
>


-- 
ANJAN PURKAYASTHA, PhD.
Senior Computational Biologist
==========================

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==========================