Re: [mart-dev] Creating a single dataset for multiple species

[Syed Haider]

Hi Joachim,

I see that that your xmls are created by lots of manual editing and 
somewhere during the process the links between template and configs are 
lost, usually MartEditor is supposed to take care of this if the XMLs 
are created automatically by the tool. Anyways, since you only have 4 
datasets, could you please share with us the mart dump if its of 
reasonable size or can we access your mart db otherwise ?

thanks
Syed


Joachim Baran wrote:
Hello!

2009/8/13 Junjun Zhang <junjun.zh...@oicr.on.ca>:
Thanks Richard. Yes, please try this first. If leaving includeDatasets empty in 
the registry doesn't help, please send me the xml files.
The includeDatasets is empty, but perhaps the following output from
'perl bin/configure.pl ...' makes more sense to you:

...
[NEW CONFIGURATION] .... WITH MEMORY [default]
default ... My Mart 55 (unstable) ...  001/004 ... btaurus_my_ensembl
................ (RDBMS) 127.0.0.1:1187 ................  OK
default ... My Mart 55 (unstable) ...  002/004 ...
mmusculus_my_ensembl .............. (RDBMS) 127.0.0.1:1187
................  OK
default ... My Mart 55 (unstable) ...  003/004 ... celegans_my_ensembl
............... (RDBMS) 127.0.0.1:1187 ................  OK
default ... My Mart 55 (unstable) ...  004/004 ... hsapiens_my_ensembl
............... (RDBMS) 127.0.0.1:1187 ................  OK
default ... Vega Mart 54 (stable) .... 001/002 ... hsapiens_gene_vega
........................ (RDBMS) 127.0.0.1:1188 ................  OK
default ... Vega Mart 54 (stable) .... 002/002 ... mmusculus_gene_vega
....................... (RDBMS) 127.0.0.1:1188 ................  OK
...
Compiling templates for visible datasets
[1/3] Attribute Panel of Dataset.. :hsapiens_my_ensembl
[1/3] Filter Panel of Dataset..... :hsapiens_my_ensembl
[2/3] Attribute Panel of Dataset.. :hsapiens_gene_vega
[2/3] Filter Panel of Dataset..... :hsapiens_gene_vega
[3/3] Attribute Panel of Dataset.. :mmusculus_gene_vega
[3/3] Filter Panel of Dataset..... :mmusculus_gene_vega

I am puzzled that the script detects the datasets of the various
species above, but then compiles the templates only for humans.
Perhaps this is how it should be, but I am not sure.

Thanks,
Joachim