Hi Charles,
Firstly, the Proserver component in the BioMart source code is
deprecated and not functional at all. Please do not use, i dont think
its document anywhere in project docs. BioMart DAS server is elsewhere
in the source and is documented in detail in project docs.
Could you please tell us which DAS features in particular are you
looking for ?
Thanks
Syed
On 08/11/2010 10:43, Charles Imbusch wrote:
Hi Syed,
I would like to use the combination of BioMart / ProServer / GBrowse to
maintain and visualize
genomic assemblies and maybe more data later on.
To understand how to setup BioMart / ProServer I'm using the dataset
included in
http://gmod.org/wiki/BioMart_Tutorial
With MartEditor I created an importable/exportable pair with internalName,
displayName, linkName and name set to "mypair". I set the "type" field to
"dasGene" for both. For importable I set the filters field to
"stable_id_1023" and for exportable, I set the attributes to
"stable_id_1023,seq_region_start_1020,seq_region_end_1020,biotype_1020,source_1018".
For the ProServer configuration, I set:
feature_keys = id,start,end,type,method
Calling ProServer from a webbrowser causes an error:
Use of uninitialized value $call in string eq at
blib/lib/Bio/Das/ProServer.pm line 859.
Connection parameters of [My BioMart Database] [ OK ]
default ... My BioMart Database ...... 001/001 ... mydemo
.................................... (RDBMS) localhost:3306
................ OK
Setting possible links between datasets
....(scanning) 100%
....(linking) 100%
....(sorting) 100%
....(clustering) 1/1 - 0 remain
....(resolving) 100%
Error building adaptor 'Bio::Das::ProServer::SourceAdaptor::biomart' for
'mymart1': Can't call method "getImportables" on an undefined value at
/usr/local/share/perl/5.10.0/Bio/Das/ProServer/SourceAdaptor/biomart.pm
line 84.
at blib/lib/Bio/Das/ProServer.pm line 794
Okay, this is not an BioMart specific, but maybe someone has a clue what's
going on.
Cheers,
Charles
