[DAS] LDAS/DasClient problems

[Mr Dmitriy Ryaboy]

Hi everyone,
I've been trying to set up a DAS annotation server at
http://zilla.lbl.gov/cgi-bin/das , but I keep running
into some problems..  I installed LDAS following
Lincoln Stein's excellent instructions, and using
slightly different test data (see below, along with
the .conf file).  Ldasdump works, http query work.  
When I try to view the annotation on Ensembl's
DasClient, however, I get the following error:

org.biojava.bio.BioError: Assertion failure: types
fetch hasn't happened yet
	at
org.biojava.bio.program.das.DASFeatureSet.getTypesMap(DASFeatureSet.java:104)

followed by the stack trace.

When I try to view it via the ensembl browser using
the "my data" option, it simply does not show up..

Any idea what could be happenning? Is it LDAS or
DasClient acting up?


Thanks for your help.

Dmitriy V Ryaboy



Data file:

[reference_points]
7	Chromosome	163792587

[annotations]
Contig	Contig_num	noncoding	Zilla	7	71902664	71904609
.	.	89.4	1	1949
Contig	Contig_num	noncoding	Zilla	7	71904635	71906190
.	.	88.8	1950	3545
Contig	Contig_num	noncoding	Zilla	7	71906197	71906593
.	.	91.5	3658	4052
Contig	Contig_num	noncoding	Zilla	7	71906903	71908121
.	.	88.4	4057	5209
Contig	Contig_num	noncoding	Zilla	7	71909258	71910351
.	.	90.1	5213	6321
Contig	Contig_num	noncoding	Zilla	7	71911326	71913995
.	.	88.2	6347	9034
Contig	Contig_num	noncoding	Zilla	7	71914014	71914195
.	.	81.7	9557	9757
Contig	Contig_num	noncoding	Zilla	7	71914208	71914666
.	.	92.2	10071	10529
Contig	Contig_num	UTR	Zilla	7	71914667	71916753	.	.
90.5	10530	12649

#followed by more of the same



.conf file

[DATA SOURCE]
description = Test annotations
adaptor     = dbi::mysqlopt
mapmaster   =
http://servlet.sanger.ac.uk:8080/das/ensembl130
database    = dastest
fasta_files =
user        = cgi
passwd      =

[CATEGORIES]
default       = structural
translation   = stop ATG CDS 5'UTR 3'UTR
misc_translated
transcription = exon intron transcript tRNA mRNA ncRNA
5'Cap TSS 
		PolyA Splice5 Splice3 misc_transcribed
variation     = insertion deletion substitution
misc_variation
structural    = Component clone primer_left
primer_right oligo assembly_tag misc_structural
similarity    = similarity NN NP PN PP misc_similarity
misc_homology noncoding
repeat        = microsatellite inverted tandom
transposable_element LINE misc_repeat
experimental  = knockout expression_tag microarrayed
RNAi_result RNAi transgenic mutant misc_experimental

# information necessary for making links from das
client to web site
[LINKS]
#default    =
http://stein.cshl.org/cgi-bin/test-cgi.pl?name=$name;class=$class;type=$type
#exon       =
http://stein.cshl.org/cgi-bin/test-cgi.pl/exon?name=$name;class=$class
#transcript =
http://stein.cshl.org/cgi-bin/test-cgi.pl/transcript?name=$name;class=$class
#insertion  =
http://stein.cshl.org/cgi-bin/test-cgi.pl/insertion?name=$name;class=$class
default     = http://zilla.lbl.gov
exon 	    = http://zilla.lbl.gov
UTR	    = http://www-gsd.lbl.gov
noncoding   = http://pga.lbl.gov

# map annotation types
[COMPONENTS]
entry_points = Component:Chromosome Component:Link
Component:Contig
has_subparts = Component:Chromosome Component:Link
has_superparts = Component:Link Component:Contig

# filters to include and/or exclude certain feature
types
[FILTER]
include = 
exclude =

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