[BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb

[Nick Matzke]

I know my issue is fixed, but just for completeness...

Hilmar Lapp wrote:
> 
> On Sep 3, 2008, at 2:16 PM, Nick Matzke wrote:
> 
>> [...]
>> mws2:~ nick$ perldoc -l DBI
>>
>> /usr/local/ActivePerl-5.10/site/lib/Bundle/DBI.pm
> 
> Can you pull up this file in an editor and see what's in there? I think 
> this may just be the CPAN bundle definition (which modules to install 
> together), but not the actual DBI module itself.
> 
>>
>> mws2:~ nick$ sudo perldoc -l DBI
>> Password:
>>
>> /usr/local/ActivePerl-5.10/site/lib/DBI.pm
> 
> If you inspect this one, it will probably be the actual DBI module.
> 
> So I suspect that your Perl module search paths aren't the same between 
> executing as root or not. If you do 'perl -V' (capital-v) you will see 
> the include path array (@INC) printed at the end. It should be identical 
> whether under sudo or not, but I suspect that for you it will not be the 
> same.

This was indeed true.  I couldn't figure out how to fix it though.  It 
appears that sudo doesn't read the .bash_profile file where I have 
additions to the PERL5LIB environmental variable.  Do you know of a way 
to get sudo to read the standard environmental variables or something 
like that?

Cheers! Thanks again for the help!
Nick



> If that's indeed the case then the question is why is the path 
> different. As the one for you as normal user is wrong, you can look into 
> your shell initialization files (.tcshrc, .cshrc for csh/tcsh; .profile, 
> .bash_profile, .login for bash) whether you see anything there that aims 
> to mess with PERL5LIB.
> 
> Or simply do 'echo $PERL5LIB' w/ and w/o sudo. Should be the same.
> 
>     -hilmar
> 

-- 
====================================================
Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
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