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Hello everyone,<br>
<br>
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.<br>
<br>
The perl script basically connects to the DB and uses the slice
method to retrieve some information. If I run this perl script<br>
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<br>
(because I am trying to develop a web based tool), the MySQL
connection fails. <br>
<br>
Error message in httpd/error_log:<br>
<blockquote> DBI
connect('host=ensembldb.ensembl.org;port=5306','anonymous',...)
failed: Can't connect to MySQL server on<br>
'ensembldb.ensembl.org' (13) at
/var/www/cgi-bin/tll_blat/ensembl-src/ensembl/modules/Bio/EnsEMBL/Registry.pm
line 1452<br>
Can't call method "selectall_arrayref" on an undefined value at<br>
/var/www/cgi-bin/tll_blat/ensembl-src/ensembl/modules/Bio/EnsEMBL/Registry.pm
line 1455.<br>
</blockquote>
<br>
I have explicitly set the location of the ensembl and perl modules
at the top of my perl script as follows:<br>
<blockquote>use warnings;<br>
<br>
use lib '/var/www/cgi-bin/tll_blat/ensembl-src/bioperl-1.2.3';<br>
use lib '/var/www/cgi-bin/tll_blat/ensembl-src/ensembl/modules';<br>
<br>
use Bio::EnsEMBL::Registry;<br>
<br>
$registry = 'Bio::EnsEMBL::Registry';<br>
$slice='Bio::EnsEMBL::Slice';<br>
$gene='Bio::EnsEMBL::Gene';<br>
<br>
$registry->load_registry_from_db(-host =>
'ensembldb.ensembl.org', -user => 'anonymous');<br>
<br>
</blockquote>
All this works when I run it from command line, but not via the web.<br>
Where could I be going wrong...?<br>
<br>
Thank you so much!<br>
<br>
~ Natascha<br>
<br>
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