[Bioperl-l] bp_seqfeature_load.pl fails on Mac os. Please help.
scott at scottcain.net
Tue Aug 24 15:04:04 EDT 2010
The file you found is not DBD::mysql though; it is
Bio::DB::SeqFeature::Store::DBI::mysql, which was installed along with
BioPerl. How did you find that file? The same method presumably
would turn up DBD::mysql if it existed. I would use a command like
which would locate all of the instances of files name mysql.pm on your
computer. I would expect it to be located in
/Library/Perl/5.8.6/darwin-thread-multi-2level/DBD/ if it was
installed in a "normal" way (that is, not involving macports or fink
On Tue, Aug 24, 2010 at 2:56 PM, Minh Bui <buiduyminh at gmail.com> wrote:
> 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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Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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