[Bioperl-l] bp_seqfeature_load.pl fails on Mac os. Please help.

Adam Witney awitney at sgul.ac.uk
Sat Aug 21 06:39:10 EDT 2010

On 20 Aug 2010, at 22:29, Minh Bui wrote:

> Hi,,
> I am trying to load my GFF file to mysql database but I got this error
> when I ran the bp_seqfeature_load.pl ( bioperl 1.6.1 on  MAC)
> [BioComplexity-5:/usr/local/bin] minh% perl bp_seqfeature_load.pl
> install_driver(mysql) failed: Can't locate DBD/mysql.pm in @INC (@INC
> contains: /sw/lib/perl5 /sw/lib/perl5/darwin
> /System/Library/Perl/5.8.6/darwin-thread-multi-2level
> /System/Library/Perl/5.8.6
> /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6
> /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level
> /Network/Library/Perl/5.8.6 /Network/Library/Perl
> /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at (eval 44)
> line 3.
> Perhaps the DBD::mysql perl module hasn't been fully installed,
> or perhaps the capitalisation of 'mysql' isn't right.
> Available drivers: DBM, ExampleP, File, Gofer, Proxy, Sponge.
> at /Library/Perl/5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 212
> I am using MAC OSX version 10.4.10 and MAMP? Isnt it the
> "/Library/Perl/5.8.6" already in @INC? What am I missing?
> I have been googling this error for a few hours. I also install
> Bioperl and reinstall DBD::mysql using CPAN. It still doesnt work..
> Here is my $PERL5LIB:  /sw/lib/perl5:/sw/lib/perl5/darwin/

Where did DBD:mysql get installed? can you verify that DBD/mysql.pm is actually in one of those directories listed above?

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