Hi, I installed the biomart perl API (biomart-perl) in order to retrieve some queries from the Phytozome mart server.
But when I intend to use the automatically generated script with the registry at http://www.biomart.org/biomart/martservice?type=registry I got the following output/Stack: ------------------------------------------------------------------------------------------------------------------------ $ perl get_exons_from_mart.pl Connection parameters of [ENSEMBL 56 GENES (SANGER UK)] [ OK ] Connection parameters of [ENSEMBL 56 VARIATION (SANGER UK)] [ OK ] Connection parameters of [ENSEMBL 56 FUNCTIONAL GENOMICS (SANGER UK)] [ OK ] Connection parameters of [VEGA 36 (SANGER UK)] [ OK ] Connection parameters of [ENSEMBL 56 GENOMIC FEATURES (SANGER UK)] [ OK ] Connection parameters of [ENSEMBL 56 ONTOLOGY (SANGER UK)] [ OK ] Connection parameters of [ENSEMBL 56 SEQUENCE (SANGER UK)] [ OK ] Connection parameters of [MSD PROTOTYPE (EBI UK)] [ OK ] Connection parameters of [ENSEMBL BACTERIA 3 (EBI UK)] [ OK ] Connection parameters of [ENSEMBL FUNGAL 3 (EBI UK)] [ OK ] Connection parameters of [ENSEMBL METAZOA 3 (EBI UK)] [ OK ] Connection parameters of [ENSEMBL PLANT 3 (EBI UK)] [ OK ] Connection parameters of [ENSEMBL PROTISTS 3 (EBI UK)] [ OK ] Connection parameters of [HIGH THROUGHPUT GENE TARGETING AND TRAPPING (SANGER UK)] [ OK ] Connection parameters of [REACTOME (CSHL US)] [ OK ] Connection parameters of [WORMBASE (CSHL US)] [ OK ] Connection parameters of [DICTYBASE (NORTHWESTERN US)] [ OK ]Optional setting for martUser in MartURLLocation location:biomart not defined - setting to default values Connection parameters of [MGI (JACKSON LABORATORY US)] [ OK ]Optional setting for includeDatasets in MartURLLocation location:biomart not defined - setting to default values Connection parameters of [CYANOBASE (KAZUSA JAPAN)] [ OK ] Connection parameters of [RGD GENES (MCW US)] [ OK ] Connection parameters of [RGD IPI MART (MCW US)] [ OK ] Connection parameters of [RGD MICROSATELLITE MARKERS (MCW US)] [ OK ]Optional setting for martUser in MartURLLocation location:g4public not defined - setting to default values Connection parameters of [HGNC (EBI UK)] [ OK ] Connection parameters of [PRIDE (EBI UK)] [ OK ] Connection parameters of [INTERPRO (EBI UK)] [ OK ] Connection parameters of [UNIPROT (EBI UK)] [ OK ] Connection parameters of [EURATMART (EBI UK)] [ OK ] Connection parameters of [PARAMECIUM GENOME (CNRS FRANCE)] [ OK ] Connection parameters of [EUREXPRESS (MRC EDINBURGH UK)] [ OK ] Connection parameters of [PEPSEEKER (UNIVERSITY OF MANCHESTER UK)] [ OK ] Connection parameters of [DB_POTATO (INTERNATIONAL POTATO CENTER-CIP)] [ OK ] Connection parameters of [DB_SWEETPOTATO (INTERNATIONAL POTATO CENTER-CIP)] [ OK ] Connection parameters of [PHYTOZOME (JGI / CIG US)] [ OK ] Connection parameters of [Sequences] [ OK ] Connection parameters of [PANCREATIC EXPRESSION DATABASE (INSTITUTE OF CANCER UK)] [ OK ] Connection parameters of [Human genome sequence] [ OK ] Connection parameters of [GRAMENE 30 ENSEMBL GENES] [ OK ] Connection parameters of [SEQUENCE] [ OK ] Connection parameters of [GRAMENE 30 MARKERS] [ OK ] Connection parameters of [GRAMENE 30 MAPPINGS] [ OK ] Connection parameters of [GRAMENE 30 QTL DB] [ OK ]Optional setting for martUser in MartURLLocation location:biomart not defined - setting to default values Connection parameters of [MGI (JACKSON LABORATORY US)] [ OK ]Optional setting for includeDatasets in MartURLLocation location:biomart not defined - setting to default values Connection parameters of [CYANOBASE (KAZUSA JAPAN)] [ OK ] could not load module BioMart::Dataset::Problem retrieving datasets for mart biomart, check your parameters: syntax error at (eval 700) line 1, near "require BioMart::Dataset::Problem retrieving datasets " Trace begun at /bio/biomart/biomart-perl/lib/BioMart/Root.pm line 191 BioMart::Root::loadModule('BioMart::Initializer=HASH(0xdf59170)', 'BioMart::Dataset::Problem retrieving datasets for mart biomart, check your parameters') called at /bio/biomart/biomart-perl/lib/BioMart/Initializer.pm line 1162 BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0xdf59170)') called at /bio/biomart/biomart-perl/lib/BioMart/Initializer.pm line 228 BioMart::Initializer::_init('BioMart::Initializer=HASH(0xdf59170)', 'registryFile', '/bio/biomart/biomart-perl/conf/biomart_registry.xml', 'action', 'clean') called at /bio/biomart/biomart-perl/lib/BioMart/Initializer.pm line 377 BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0xdf59170)', 'registryFile', '/bio/biomart/biomart-perl/conf/biomart_registry.xml', 'action', 'clean') called at /bio/biomart/biomart-perl/lib/BioMart/Initializer.pm line 144 BioMart::Initializer::_new('BioMart::Initializer=HASH(0xdf59170)', 'registryFile', '/bio/biomart/biomart-perl/conf/biomart_registry.xml', 'action', 'clean') called at /bio/biomart/biomart-perl/lib/BioMart/RootI.pm line 64 BioMart::RootI::new('BioMart::Initializer', 'registryFile', '/bio/biomart/biomart-perl/conf/biomart_registry.xml', 'action', 'clean') called at get_exons_from_mart.pl line 17 ------------------------------------------------------------------------------------------------------------------------ I've installed mod_perl, apxs (http-devel), martj-0.7. , but fail to run successfully any of the sample scripts/databases. I see there is nothing wrong with the queries in the script, but it stops when dealing with the BioMart::Initializer object, so the script does not even try the queries. For now I am really interested in running queries in the external Phytosome server ( I don't want to run a mart db on my own), any help???
