[Bioperl-l] about git and perl5lib

Dave Messina David.Messina at sbc.su.se
Fri Oct 29 08:18:40 EDT 2010


There's a minor inconsistency on our part: the path to the bioperl-run modules is actually bioperl-run/lib


Note that bioperl-live will I believe also be switching to this at some point; having the modules in a lib subdir is standard Perl practice.


Dave






On Oct 29, 2010, at 4:29, Dimitar Kenanov <dimitark at bii.a-star.edu.sg> wrote:

> Hi guys,
> i am sorry if this sounds stupid but i have problem with the PERL5LIB and the GIT version of BioPerl(BP). I downloaded the BP-live and BP-run from git. I use Slackware so I added the following line in bashrc:
> 
> export PERL5LIB=$HOME/Bioperl_git/bioperl-live:$HOME/Bioperl_git/bioperl-run:$PERL5LIB
> 
> But when i start a script using StandAloneBlastPlus i see perl cant find it:
> 
> Can't locate Bio/Tools/Run/StandAloneBlastPlus.pm in @INC (@INC contains: /home/domine/Bioperl_git/bioperl-live /home/domine/Bioperl_git/bioperl-run /usr/lib64/perl5/5.10.1/x86_64-linux-thread-multi /usr/lib64/perl5/5.10.1 /usr/lib64/perl5/site_perl/5.10.1/x86_64-linux-thread-multi /usr/lib64/perl5/site_perl/5.10.1 /usr/lib64/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.10.1/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.10.1 /usr/lib64/perl5/vendor_perl
> 
> It seems Perl should find the module but it doesnt. Any idea where i could have made a mistake?
> 
> Btw with:  perl -MBio::Perl -le 'print Bio::Perl->VERSION;' i get 1.0069
> 
> Thank you
> Dimitar
> 
> 
> 
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