Hi Fausto,
the Phytozome and Cynbase entry in registry needs to be fixed, we will
do it next week. For now, could you please modify the MartURLLocation
entries in the registry (there are two for Phytozome) and set the property:
host="www.biomart.org"
to
host="www.phytozome.net"
Also, where you see the MartURLLocation entry for Cynobase, do this:
host="www.biomart.org"
to
host="mart.kazusa.or.jp"
we hope to fix it during this week.
Best
Syed
Fausto RodrÃguez Zapata wrote:
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???
