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 _______________________________________________ DAS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/das
