[Gmod-schema] Errors in make prepdb

[Michael D. <mic...@bc...>]

Hi,

I am installing chado 1.2 on MacOS 10.8, perl 5.12.3, following the INSTALL.chado manual and have managed to do 
make load_schema

When I run make prepdb I get following error:

BEGIN failed--compilation aborted at bin/gmod_add_organism.pl line 7.
Adding Daphnia pulex to the database...
Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at bin/gmod_add_organism.pl line 7.
BEGIN failed--compilation aborted at bin/gmod_add_organism.pl line 7.

It looks like some developer's home directories got checked in, where there should in fact be "./lib/". So I tried:
export PERL5LIB=./blib/lib/:./lib

But that yields a new error:

…
Can't locate Bio/Chado/Schema.pm in @INC (@INC contains: /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib ./blib/lib/ ./lib /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at bin/gmod_add_organism.pl line 9.
BEGIN failed--compilation aborted at bin/gmod_add_organism.pl line 9.
Confucius:chado-1.2 mdondrup$ 

And there is indeed no such module present in the package.

Best

Michael Dondrup
Post-doctoral researcher
The Sea Lice Research Centre
Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen, 
Norway