[ensembl-dev] Getting import_vcf.pl working

[Tchourbanov, Alexander Y - (atchourb)]

Dear ENSEMBL developers,

When I try to download VCF file to the locally installed database using the following command:

perl ./import_vcf.pl -i ./common_all.vcf.gz -db VCFdump -u atchourb --password abcd1234 --source dbSNP --population general

I get the following message:

Use of qw(...) as parentheses is deprecated at /usr/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 1564.
2013-02-22 16:33:54 - Session ID is a9703281edc05675ba906f396b0586fb
human is not a valid species name for this instance
Use of uninitialized value $species in hash element at /usr/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 958.
Use of uninitialized value $species in hash element at /usr/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 969.
ERROR: Could not get population adaptor

What is the way to get the population adapter? Are there more detailed instructions on how to download de novo VCF file to a database with import_vcf.pl?

Another question refers to usage of the registry file, which I never managed to get working:

use strict;

use Bio::EnsEMBL::Utils::ConfigRegistry;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;

new Bio::EnsEMBL::DBSQL::DBAdaptor(
  -user    => 'atchourb',
  -pass => 'abcd1234',
  -host    => 'localhost',
  -port    => '3306',
  -dbname  => 'VCFdump'
);

my @aliases = ( 'H_Sapiens', 'human' );

Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
  -species => 'Homo sapiens',
  -alias   => \@aliases
);

after running the program I get the following message:

Use of qw(...) as parentheses is deprecated at /usr/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 1564.
2013-02-22 16:40:30 - Session ID is dd2fc7598559030f21bfcc9bc529162f
./registry.conf did not return a true value at /usr/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 360.

Thanks for any suggestions!

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