Hi Michele There exist dataset naming conflict in pancreasMart and EnsemblMart. You need to keep them separately in two different virtual schemas. The two groups which would not results in conflict are :
======================================== GROUP 1: should belong to one virtual schema ======================================== <MartURLLocation database="ensembl_mart_45" default="1" displayName="ENSEMBL 45 GENES (SANGER)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" /> <MartURLLocation database="compara_mart_homology_45" default="0" displayName="ENSEMBL 45 HOMOLOGY (SANGER)" host="www.biomart.org" includeDatasets="" martUser="" name="compara_mart_homology_45" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" /> <MartURLLocation database="compara_mart_pairwise_ga_45" default="0" displayName="ENSEMBL 45 PAIRWISE ALIGNMENTS (SANGER)" host="www.biomart.org" includeDatasets="" martUser="" name="compara_mart_pairwise_ga_45" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" /> <MartURLLocation database="compara_mart_multiple_ga_45" default="0" displayName="ENSEMBL 45 MULTIPLE ALIGNMENTS (SANGER)" host="www.biomart.org" includeDatasets="" martUser="" name="compara_mart_multiple_ga_45" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" /> <MartURLLocation database="snp_mart_45" default="0" displayName="ENSEMBL 45 VARIATION (SANGER)" host="www.biomart.org" includeDatasets="" martUser="" name="snp" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" /> <MartURLLocation database="sequence_mart_45" default="0" displayName="ENSEMBL 45 SEQUENCE (SANGER)" host="www.biomart.org" includeDatasets="" martUser="" name="sequence" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="0" /> <MartURLLocation database="vega_mart_45" default="0" displayName="VEGA 21 (SANGER)" host="www.biomart.org" includeDatasets="" martUser="" name="vega" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" /> <MartURLLocation database="uniprot_mart_17" default="0" displayName="UNIPROT PROTOTYPE (EBI)" host="www.biomart.org" includeDatasets="" martUser="" name="uniprot" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" /> <MartURLLocation database="msd_mart_4" default="0" displayName="MSD PROTOTYPE (EBI)" host="www.biomart.org" includeDatasets="" martUser="" name="msd" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" /> <MartURLLocation default="0" displayName="GRAMENE (CSHL)" host="www.gramene.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/Multi/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" /> <MartURLLocation database="wormmart_176" default="1" displayName="WORMBASE (CSHL)" host="www.wormbase.org" includeDatasets="" martUser="" name="wormbase176" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" /> <MartURLLocation default="0" displayName="DICTYBASE (NORTHWESTERN)" host="www.dictybase.org" includeDatasets="" martUser="" name="dicty" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="dictyMart" visible="1" /> <MartURLLocation default="" displayName="RGD GENES (MCW)" host="rote.hmgc.mcw.edu" includeDatasets="rgd_genes" martUser="" name="rgd_mart" path="/biomart/martservice" port="9999" redirect="1" serverVirtualSchema="default" visible="1" /> <MartURLLocation default="" displayName="RGD MICROSATELLITE MARKERS (MCW)" host="rote.hmgc.mcw.edu" includeDatasets="SSLP" martUser="" name="SSLP_mart" path="/biomart/martservice" port="9999" redirect="1" serverVirtualSchema="default" visible="1" /> <MartURLLocation database="pepseekerGOLD_mart" default="0" displayName="PEPSEEKER (UNIVERSITY OF MANCHESTER)" host="www.ispider.manchester.ac.uk" includeDatasets="peptide_1" martUser="" name="pepseekerGOLD_mart" path="/pepseeker/biomart/martservice" port="80" redirect="1" serverVirtualSchema="pepseekerGOLD" visible="1" /> <MartURLLocation database="pride_mart_2" default="1" displayName="PRIDE (EBI)" host="www.ebi.ac.uk" includeDatasets="" martUser="" name="pride" path="/pride/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" /> ======================================== GROUP 2: should belong to another virtual schema ======================================== <MartURLLocation database="gene_test_41_v02_p80" default="" displayName="PANCREATIC EXPRESSION DATABASE (INSTITUTE OF CANCER)" host="www.pancreasexpression.org" includeDatasets="" martUser="" name="Pancreatic_Expression" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" /> <MartURLLocation database="seq_test_41" default="" displayName="Human genome sequence" host="www.pancreasexpression.org" includeDatasets="" martUser="" name="SEQ" path="/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="0" /> In addition, are you sure you really want to configure the complete registry as on Biomart central server. Its a huge registry and need substantial time to configure. You may also drop one of the conflicting marts if you do not need both. hope this would work for you. regards syed On Thu, 2007-07-26 at 14:55 +0200, Michele Muggiri wrote: > Hi, i try to install biomart-perl and all is ok, bat when i try to use > the registry downloaded from > http://www.biomart.org/biomart/martservice?type=registry with the > command > "# perl bin/configure.pl -r conf/registry.xml" > hi return me this message: > > " > > ERROR something wrong with your registry: > Dataset 'gaculeatus_gene_ensembl' is duplicated in > virtualSchema > 'BioMart::Configuration::VirtualSchema=HASH(0x9992840)->name' > Please rename datasets in meta_conf tables or separate > conflicting datasets > into different virtual schemas in > defaultMartRegistry.xml > > > Trace begun > at /usr/local/biomart-perl/bin/../lib/BioMart/Initializer.pm line 1150 > BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x98fdb10)') > called at /usr/local/biomart-perl/bin/../lib/BioMart/Initializer.pm line 244 > BioMart::Initializer::_init('BioMart::Initializer=HASH(0x98fdb10)', > 'registryFile', '/usr/local/biomart-perl/conf/registry.xml', 'action', > 'cached', 'mode', 'memory') called > at /usr/local/biomart-perl/bin/../lib/BioMart/Initializer.pm line 393 > BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x98fdb10)', > 'registryFile', '/usr/local/biomart-perl/conf/registry.xml', 'action', > 'cached', 'mode', 'memory') called at > /usr/local/biomart-perl/bin/../lib/BioMart/Initializer.pm line 344 > BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x98fdb10)', > 'registryFile', '/usr/local/biomart-perl/conf/registry.xml', 'action', > 'cached', 'mode', 'memory') called at > /usr/local/biomart-perl/bin/../lib/BioMart/Initializer.pm line 184 > BioMart::Initializer::_new('BioMart::Initializer=HASH(0x98fdb10)', > 'registryFile', '/usr/local/biomart-perl/conf/registry.xml', 'action', > 'cached', 'mode', 'memory') called > at /usr/local/biomart-perl/bin/../lib/BioMart/RootI.pm line 42 > BioMart::RootI::new('BioMart::Initializer', 'registryFile', > '/usr/local/biomart-perl/conf/registry.xml', 'action', 'cached', > 'mode', 'memory') called > at /usr/local/biomart-perl/bin/configureBioMart.pl line 302 > eval {...} at /usr/local/biomart-perl/bin/configureBioMart.pl line 301 > " > > you can help me? -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
