[Bioperl-l] bp_seqfeature_load.pl fails on Mac os. Please help.
buiduyminh at gmail.com
Tue Aug 24 14:56:43 EDT 2010
How can I know where DBD:mysql PATH on my MAC? I am very new to MAC sorry.
I just check and mysql.pm is in
On 8/21/10, Adam Witney <awitney at sgul.ac.uk> wrote:
> 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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