[ensembl-dev] Problem with using ensembl API when called via the web

[Natascha May]

Hello everyone,

I am new to using the ensembl perl API (version 63). I would really 
appreciate some help for a problem I'm having with my perl script.

The perl script basically connects to the DB and uses the slice method 
to retrieve some information. If I run this perl script
from my terminal, it works fine, and I am able to get results from 
ensembl. However, if I call this perl script via a php script
(because I am trying to develop a web based tool), the MySQL connection 
fails.

Error message in httpd/error_log:

    DBI connect('host=ensembldb.ensembl.org;port=5306','anonymous',...)
    failed: Can't connect to MySQL server on
    'ensembldb.ensembl.org' (13) at
    /var/www/cgi-bin/tll_blat/ensembl-src/ensembl/modules/Bio/EnsEMBL/Registry.pm
    line 1452
    Can't call method "selectall_arrayref" on an undefined value at
    /var/www/cgi-bin/tll_blat/ensembl-src/ensembl/modules/Bio/EnsEMBL/Registry.pm
    line 1455.


I have explicitly set the location of the ensembl and perl modules at 
the top of my perl script as follows:

    use warnings;

    use lib '/var/www/cgi-bin/tll_blat/ensembl-src/bioperl-1.2.3';
    use lib '/var/www/cgi-bin/tll_blat/ensembl-src/ensembl/modules';

    use Bio::EnsEMBL::Registry;

    $registry = 'Bio::EnsEMBL::Registry';
    $slice='Bio::EnsEMBL::Slice';
    $gene='Bio::EnsEMBL::Gene';

    $registry->load_registry_from_db(-host => 'ensembldb.ensembl.org',
    -user => 'anonymous');

All this works when I run it from command line, but not via the web.
Where could I be going wrong...?

Thank you so much!

~ Natascha

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