[DAS] GBrowse as DAS server+Ensembl as DAS client

[Prem Anand]

Hi

We are trying to set up our GBrowse as DAS server and were testing it with
ensembl as client.

We have the right metadata in the datasource.conf file.

<COORDINATES uri="http://www.dasregistry.org/dasregistry/coordsys/CS_DS311"
authority="GRCh" test_range="chr1:114356433..114414381" taxid="9606"
version="37" source="Chromosome">GRCh_37,Chromosome,Homo
sapiens</COORDINATES>

The server responds for /cgi-bin/das/sources (also /cgi-bin/das/dsn) well.
We also tried with different capabilities locally and it seems to be fine.

In all our GFF files/gbrowse databases we name the chromosomes prefexing
with 'chr' as given in the test_range.

But ensembl client seems to ignore the test_range and is making the request
as shown below ( from http access log)

/cgi-bin/das/01_Hs_GRCh37%7CASSOC_VARIANT/features?segment=1:114355433,114415381;maxbins=872
HTTP/1.1" 200 345 "-" "Ensembl/60"


And as GBrowse server doesn't recognise the region (1:114355433,114415381),
it doesn't return anything back.
In cgi-bin/das script, approximately at around line 860, if I prefix the
$reference with 'chr', it works.

foreach (@segments) {
        my ($reference,$refclass,$start,$stop) = @$_;

        if($reference !~ /^chr/){
         $reference = "chr".$reference;
        }


We are not happy with this fix and wondering if it is a ensembl client issue
or gbrowse server issue.

Shouldn't ensembl make the right request figuring out the right url from
'test_range'?
OR
If GBrowse server has to handle it in a better way?

Any directions would help.

Many Thanks
Prem