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

[Scott Cain]

Hi Minh,

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
this:

  locate mysql.pm

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
or MAMP).

Scott


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
> /Library/Perl/5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>
>
>
> 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