Bioperl: running local blasts

[Steve Chervitz]

The LocalBlast module in the distribution is non-functional as-is. It is
intended to be customized for your local environment. From the documentation in
this module:

# PACKAGE : Bio::Tools::Blast::Run::LocalBlast.pm
# ...
# STATUS  : STUB MODULE, MUST BE CUSTOMIZED FOR A LOCAL SITE.
# ...
# This module as-is provides only framework for running Blasts locally.
# Customize it for your site. See comments below for tips.

The documentation could be clearer about this point. I'm sure more can be done
to make this module so it works with minor configuration, either via a special
config file or environment variables. Stay tuned.

Steve

Joey Morris wrote:

> Can anyone tell me if they are successfully running local blast searches
> using the LocalBlast.pm module? I just downloaded 0.6.1 and I get this error
> when running a local blast:
>
> *** 1 Blast reports produced fatal errors:
> Undefined subroutine &Bio::Root::Object::_rearrange called at
> /local/lib/perl/lib/Bio/Tools/Blast/Run/LocalBlast.pm line 309.
>
> I experienced the same issue with 0.6.0 but not with the 0.05.1 release.
> I've reported it as a bug but there's been no progess on it apparently.
>
> Thanks,
> Joey
>
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