[Bioperl-l] load_seqdatabase.pl question

Hilmar Lapp hlapp at gmx.net
Tue Nov 28 11:20:59 EST 2006

Hi Derek,

first off, I'd recommend to always post such questions to the mailing  
list; sometimes I may not have a chance to check my email for a while  
or respond right away but someone else may know the answer too.

In your case it looks like you didn't install bioperl-db. You need to  
install bioperl-db from CVS (using the main trunk). Instructions for  
how to do this are on the bioperl web site. Let me (and the list)  
know if you have trouble finding those.

Let me know if you did install bioperl-db. (If you did, did you also  
set PERL5LIB if you installed it in non-standard place, such as your  
home directory?)


On Nov 27, 2006, at 12:07 PM, Derek Buchfink wrote:

> Hi, I am new to BioSQL and I am looking to use the  
> load_seqdatabase.pl script to load some data into a PostgreSQL  
> 8.1.4 database. I am using version 1.24 of the script. However, I  
> am getting the following error:
> Can't locate Bio/DB/BioDB.pm in @INC (@INC contains: /usr/lib/ 
> perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/ 
> perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/ 
> site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/ 
> 5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386- 
> linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread- 
> multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/ 
> lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/ 
> perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/ 
> site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/ 
> site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi / 
> usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/ 
> perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/ 
> vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/ 
> vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/ 
> vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/ 
> vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/ 
> vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/ 
> vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/ 
> vendor_perl .) at load_seqdatabase.pl line 337.
> BEGIN failed--compilation aborted at load_seqdatabase.pl line 337.
> Do you know how to solve this issue or do you have any helpful  
> suggestions? Thank you very much.
> Derek Buchfink

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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