[Bioperl-l] Bioperl 1.5.2 RC2

Sendu Bala bix at sendu.me.uk
Tue Oct 17 10:00:39 EDT 2006


Niels Larsen wrote:
> Greetings,
> 
> I am no perl beginner, but I am a BioPerl beginner. Today I looked
> for remote similarity services that can be used from Perl. I found
> the EBI SOAP interface where their example script returns
> 
> Can't find method element in the message at 
> /ebi/extserv/bin/perl-5.8.3/lib/site_perl/5.8.3/SOAP/Lite.pm line 2311.

What script exactly? There was a problem with the SOAP server that was 
fixed earlier today.


> and the DDBJ service which (from Denmark) returns
> 
> undef

What returned undef? Specifics please.


> and then the NCBI server accessed through BioPerls RemoteBlast which
> seems to spin in a loop that fills TMPDIR with many tempfiles. Will
> release 1.5.2 include improvements to RemoteBlast? (I see Roger Hall
> is working towards that).

What version of Bioperl were you testing with? What did you do to get it 
to 'spin in a loop'? I can tell you that remote blasting certainly works 
in Bioperl 1.5.2, but you'll have to give more details on the things you 
tried and the problems you encountered.

You can also answer the questions yourself by trying the release candidate.


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