[Bioperl-l] Blast returns result, but does not return hits

Chris Fields cjfields at uiuc.edu
Thu Feb 23 10:23:53 EST 2006


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Raghunath Verabelli
> Sent: Wednesday, February 22, 2006 8:25 PM
> To: Chris Fields; bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Blast returns result, but does not return hits
> 
> 
> Thanks very much Chris for your time.
> Please see below output that you requested (the only
> difference i saw between your output and mine is @INC
> value. I have only 2 directories c:\mod_perl\perl
> where i installed activeperl. I see two additional
> directories in your @INC path).
> 
> >
> > When you type 'perl -V' what do you see (make sure
> > it is a capital 'V', not
> > lower case).
> 
> C:\Documents and Settings\Administrator>perl  -V
> Summary of my perl5 (revision 5 version 8 subversion
> 7) configuration:
>   Platform:
>     osname=MSWin32, osvers=5.0,
> archname=MSWin32-x86-multi-thread

[....]

> if.pm
>   Built under MSWin32
>   Compiled at Nov  2 2005 08:44:52
>   %ENV:
>     PERL5LIB="c:\bioperl-live"
>   @INC:
>     c:\bioperl-live
>     C:/mod_perl/Perl/lib
>     C:/mod_perl/Perl/site/lib
>     .

Personally I wouldn't place the the bioperl-live folder in the root
directory; this shouldn't make a difference, but you can try moving it to
the perl directory in a separate folder to see if that helps.  Can't see why
it would make a difference, but it is Windows... Main reason I'll switching
over to Mac OS X!

Make sure that the Bio directory is in the bioperl-live directory,
regardless (i.e. if PERL5LIB is set to
C:\mod_perl\Perl\bioperl\bioperl-live, then there should be a directory like
C:\Perl\bioperl\bioperl-live\Bio).  Otherwise it won't work.

What do you get with this?

perl -MBio::Root::Version -e "print $Bio::Root::Version::VERSION"

If everything is working (PERL5LIB, etc) then it should be 1.5 for CVS
bioperl; otherwise it will either find the old version (1.2.3) or fail
completely.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 




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