Hi, I replaced the file and now I get this little error when I run the example perl script from Biomart:
....(linking) 100% ....(sorting) 100% ....(clustering) 1/1 - 0 remain ....(resolving) 100% Dataset default.btaurus_snp not found in registry Should the virtualSchemaName be different in the perl script (since it's set to default right now)? I'm sorry I'm still pretty new to all of this, thank you. Dzu Quoting Syed Haider <[email protected]>: > just correcting the email client's mistake, please see below > > > > On 25/10/2010 20:10, Jonathan Guberman wrote: > > > Please replace the MartURLLocation section with the following: > > > > <MartDBLocation > > databaseType="mysql" > > host="martdb.ensembl.org<http://martdb.ensembl.org>" > > ^^^^^^ > host="martdb.ensembl.org" > > > database="snp_mart_59" > > name="snp" > > displayName="ENSEMBL VARIATION 59 (SANGER UK)" > > port="5316" > > schema="snp_mart_59" > > user="anonymous" > > password="" > > visible="1" > > default="0" > > martUser="" > > includeDatasets="" > > /> > > > > cheers > Syed > > > Jonathan Guberman, PhD > > Application Programmer > > > > Ontario Institute for Cancer Research > > MaRS Centre, South Tower > > 101 College Street, Suite 800 > > Toronto, Ontario, Canada M5G 0A3 > > > > Tel: 647-260-7818 > > Toll-free: 1-866-678-6427 > > www.oicr.on.ca<http://www.oicr.on.ca> > > > > On 2010-10-25, at 2:48 PM,<[email protected]<mailto:[email protected]>> > <[email protected]<mailto:[email protected]>> wrote: > > > > Hi all, > > > > I was wondering as I still haven't found a solid solution to this problem > yet, > > if I was able to download/query Biomart correctly with this Registry: > > > > <?xml version="1.0" encoding="UTF-8"?> > > <!DOCTYPE MartRegistry> > > <MartRegistry> > > > > <MartURLLocation > > name = "ensembl" > > displayName = "ensembl" > > host = > "www.biomart.org<http://www.biomart.org>" > > port = "80" > > visible = "1" > > default = "" > > includeDatasets = "btaurus_gene_ensembl" > > martUser = "" > > /> > > > > </MartRegistry> > > > > What exactly do I need to change in my registry in order to download from > the > > SNP database? I tried different name/displayName/includeDatasets (like > > btaurus_snp) but to no avail, please help, thank you. > > > > Dzu > > > > > > >
