<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div>Dear all,</div><div><br></div><div>I have installed a local version of the compara database named GENOCOMP (without the core(s) databases).</div><div>Then, I would like to use the perl API to query it.</div><div>Here is the simple script I used with the ensembl.init file at the end of the email.</div><div><div><br></div><div>###############</div><div><font face="Courier New">use strict;</font></div><div><font face="Courier New">use warnings;</font></div><div><font face="Courier New">use Data::Dumper;</font></div><div><font face="Courier New">use Bio::EnsEMBL::Registry;</font></div><div><font face="Courier New"><br></font></div><div><div><font face="Courier New">Bio::EnsEMBL::Registry->load_all();</font></div><div><font face="Courier New">my $member_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Compara', 'compara', 'GeneMember');</font></div></div></div><div><font face="Courier New">print Dumper $member_adaptor;</font></div><div>#################</div><div><br></div><div>This scripts returns the following error:</div><div><br></div><div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">------------------- WARNING ----------------------</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">MSG: Compara is not a valid species name (check DB and API version)</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">FILE: Bio/EnsEMBL/Registry.pm LINE: 1198</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 983</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">Date (localtime) = Fri Jul 18 11:04:36 2014</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">Ensembl API version = 75</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">---------------------------------------------------</div><div style="margin: 0px; font-size: 11px; font-family: Menlo; min-height: 13px;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">-------------------- EXCEPTION --------------------</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">MSG: Can not find internal name for species 'Compara'</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">STACK Bio::EnsEMBL::Registry::get_adaptor /home/genouest/umr6061/recomgen/tderrien/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:985</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">STACK toplevel getOrthologAPI_genocomp.pl:65</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">Date (localtime) = Fri Jul 18 11:04:36 2014</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">Ensembl API version = 75</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">---------------------------------------------------</div></div><div><br></div><div><br></div><div>I also tried with:</div><div><div><font face="Courier New">my $member_adaptor = Bio::EnsEMBL::Registry->get_adaptor(‘Multi', 'compara', 'GeneMember');</font></div></div><div>without any success.</div><div><br></div><div>Any help would be much appreciated.</div><div><br></div><div>Thanks in advance</div><div><br></div><div>Thomas</div><div><br></div><div><br></div><div><br></div><div>PS: My ensembl.init file</div><div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span style="color: #34bbc7"><b>$ </b></span>cat ~/.ensembl_init </div></div><div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">use strict;</div><div style="margin: 0px; font-size: 11px; font-family: Menlo; min-height: 13px;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">use Bio::EnsEMBL::Utils::ConfigRegistry;</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">use Bio::EnsEMBL::DBSQL::DBAdaptor;</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;</div><div style="margin: 0px; font-size: 11px; font-family: Menlo; min-height: 13px;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Menlo; min-height: 13px;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">my $host = 'genobdd';</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">my $user = 'GENOCOMP';</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">my $port = 5306;</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">my $dbname = 'GENOCOMP';</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">my $pass = ‘XXXXXXXXX';</div><div style="margin: 0px; font-size: 11px; font-family: Menlo; min-height: 13px;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Menlo; min-height: 13px;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> -host => $host, <span class="Apple-tab-span" style="white-space:pre"> </span></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> -user => $user,<span class="Apple-tab-span" style="white-space:pre"> </span></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> -pass<span class="Apple-tab-span" style="white-space:pre"> </span> => $pass,</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> -port => $port,<span class="Apple-tab-span" style="white-space:pre"> </span></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> -dbname => $dbname,<span class="Apple-tab-span" style="white-space:pre"> </span></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> -verbose => 1</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">);</div></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">1;</div></body></html>