[Bioperl-l] Can't get bioperl to install

Fields, Christopher J cjfields at illinois.edu
Fri Feb 17 22:16:18 EST 2012


The error indicates that BioPerl isn't in your @INC (paths where perl searches for modules).  There are a number of things that could cause this, namely changing the version of perl you are using, upgrades to the OS, changes in local configuration, e.g. missing PERL5LIB.  In short, anything that can possibly modify the search path.

You could possibly try adding the bioperl directory to PERL5LIB locally.  What you *don't* want to do is attempt to add a version-specific path (say, a directory for an older version of perl in the system perl library).  

See this for more details on @INC:

http://stackoverflow.com/questions/2526804/how-is-perls-inc-constructed-aka-what-are-all-the-ways-of-affecting-where-pe

chris

On Feb 17, 2012, at 8:03 PM, Joshua Levine wrote:

> Hello,
> 
> I used to have bioperl working just fine on my machine (MacBook Pro,
> running OS X v10.6.8).  I tried installing some new perl modules ( DBI &
> DBD::mysql) and have not gotten them to work yet, but when I went back to
> run a script that uses bioperl, I got this error message:
> 
> Can't locate Bio/SeqIO.pm in @INC...
> 
> Now I just want to get bioperl working again, even if I can't also get DBI
> & DBD:mysql working.
> 
> Any help would be greatly appreciated
> -Josh
> 
> 
> -- 
> Joshua A. Levine
> 
> Graduate Student
> University of Arizona
> Ecology and Evolutionary Biology
> BioScience West 121
> jalevine at email.arizona.edu
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