[Bioperl-l] BIOPERL_SAVVY?

[Brian Osborne]

Heikki,

> Other envparams: BIOPERLDEBUG, OBDA_SEARCH_PATH.

And BIOPERL_INDEX, BIOPERL_INDEX_TYPE.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of Heikki Lehvaslaiho
Sent: Monday, May 12, 2003 4:33 AM
To: Ewan Birney
Cc: Bioperl
Subject: Re: [Bioperl-l] BIOPERL_SAVVY?

Ewan,

I like the idea. We should be consistent with them and document them
clearly. Could you start a document about running bioperl?
Other envparams: BIOPERLDEBUG, OBDA_SEARCH_PATH.

At the same time we should clean the top directory and move all the *pod
files under doc directory.


Actually, we might be able to get rid of those LWP-related error
messages completely. There is a recent module Bio::Root::HTTPget which
could be used as a fallback. (I did not know about it before this
weekend).

We really need a good clean up of Bio::DB modules and logic. Volunteers
please!


        -Heikki



On Sat, 2003-05-10 at 17:25, Ewan Birney wrote:
> I have tweaked the bpfetch script so it does not fall over if LWP has not
> been installed. Currently is says this:
>
>
> bpfetch cannot find Bio::DB::GenBank and Bio::DB::EMBL modules
> This is most likely because LWP has not been installed
> This does not effect local indexing
> set environment variable BIOPERL_SAVVY to supress this message
>
>
> Is this a good idea? Should we standardise on environemnt variable to
> suppress "helpful" warning messages or not?
>
>
>
>
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--
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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