[ensembl-dev] "Can't locate DBD/mysql.pm in @INC" error

[John MC Ma]

Hi,

You'd need to install the Perl module DBD::mysql before using Ensembl
API, see http://www.ensembl.org/info/docs/api/api_installation.html.

Cheers,

John Ma
Iowa City, Iowa

On 7/12/2012 5:23 AM, Arjun Ray wrote:
> Hi,
>
> I am new to using the Ensembl API. This is the following error I am
> getting (this would be my first attempt at the API).
>
> ###########
> The API version used is 67
> install_driver(mysql) failed: Can't locate DBD/mysql.pm in @INC (@INC
> contains: /sw/lib/perl5 /sw/lib/perl5/darwin
> /Users/rayarjun/src/bioperl-live /Users/rayarjun/src/ensembl/modules
> /Users/rayarjun/src/ensembl-compara/modules
> /Users/rayarjun/src/ensembl-variation/modules
> /Users/rayarjun/src/ensembl-functgenomics/modules
> /Users/rayarjun/src/bioperl-live /Users/rayarjun/src/ensembl/modules
> /Users/rayarjun/src/ensembl-compara/modules
> /Users/rayarjun/src/ensembl-variation/modules
> /Users/rayarjun/src/ensembl-functgenomics/modules
> /Library/Perl/Updates/5.10.0
> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
> /System/Library/Perl/5.10.0
> /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0
> /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
> /Network/Library/Perl/5.10.0 /Network/Library/Perl
> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.10.0 .) at (eval 5) 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, SQLite, Sponge.
>  at /Users/rayarjun/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 1576
>
> ##########################################
>
> The script is pasted below :
>
> #######################
> use strict;
> use warnings;
>
> use Bio::EnsEMBL::Registry;
> use Bio::EnsEMBL::ApiVersion;
> printf( "The API version used is %s\n", software_version() );
>
> my $registry = 'Bio::EnsEMBL::Registry';
> $registry->load_registry_from_db(
>    -host => 'ensembldb.ensembl.org',
>    -user => 'anonymous',
>    -port => 3306,
>    -db_version => 67,
> );
>
> my $adaptor = $registry->get_adaptor( 'Human', 'Core', 'Transcript' );
>
> my $transcript =
> $adaptor->fetch_by_translation_stable_id('ENSP00000261584');
>
> print $transcript->display_id."\n";
>
> #####################
>
>
> Regards
>
> Arjun
>
>
>
>
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