Please send me your perl script and registry file (off the list),
thanks
Syed
On 26/10/2010 17:45, vile...@vt.edu wrote:
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<syed.hai...@oicr.on.ca>:
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,<vile...@vt.edu<mailto:vile...@vt.edu>>
<vile...@vt.edu<mailto:vile...@vt.edu>> 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
