[DAS] Help setting up LDAS

[Lincoln Stein]

Hi Ben,

This is interesting.  Could you send me ls -l of the configuration directory? 
 It may be something as simple as permissions on the dicty.conf file.

Lincoln


On Friday 07 December 2001 11:49, Benjamin L. King wrote:
> Hello,
>
> I'm in the process of setting up a LDAS server and need some help with
> its configuration on the web side of things.
>
> I've been following the LDAS installation instructions and am trying to
> test it using test data from the distribution.  I've got all the
> required products running and tested (as far as I can tell).  The
> following 'dsn' query does not show my test database, named 'dicty'.
> Instead it returns information about the other DAS servers (C.Elegans and
> the test.org DAS server).
>
> http://crick.informatics.jax.org:8080/cgi-bin/das/dsn
>
> Here's the results of the query:
>
> Date: Fri, 07 Dec 2001 16:49:03 GMT
>  Server: Apache/1.3.22 (Unix)
>  x-das-status: 200 OK
>  x-das-version: DAS/1.00
>  Connection: close
>  Content-Type: text/plain; charset=ISO-8859-1
>
>  <?xml version="1.0" standalone="yes"?>
>  <!DOCTYPE DASDSN SYSTEM "http://www.biodas.org/dtd/dasdsn.dtd">
>  <DASDSN>
>     <DSN>
>        <SOURCE id="elegans">elegans</SOURCE>
>        <MAPMASTER>http://www.wormbase.org/db/das/elegans</MAPMASTER>
>        <DESCRIPTION>C. elegans annotations on chromosome I &
> II</DESCRIPTION>
>     </DSN>
>     <DSN>
>        <SOURCE id="test">test</SOURCE>
>        <MAPMASTER>http://www.test.org/db/das/dicty</MAPMASTER>
>        <DESCRIPTION>Test annotations</DESCRIPTION>
>     </DSN>
>  </DASDSN>
>
>
> I have a dicty.conf file (copied from test.conf in the LDasServer 1.0
> distribution).  It's DATASOURCE parameters are:
>
> [DATA SOURCE]
> description = Test annotations
> adaptor     = dbi::mysqlopt
> mapmaster   = http://crick.informatics.jax.org:8080/cgi-bin/das/dicty
> database    = dicty
> fasta_files =
> user        = nobody
> passwd      = xxxxxxx   (I x'ed this out on purpose)
>
> Does anyone have any suggestions?
>
> Since my 'dicty' database was loaded only with the test data, can it
> server as a reference server (mapmaster parameter)?  Is there some other
> test reference server that I could use instead?
>
> Thank you,
>
> - Ben
>
> Benjamin L. King
> Mouse Genome Informatics
> The Jackson Laboratory
> Bar Harbor, ME  04609  USA
>
> blk@informatics.jax.org
>
>
>
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY

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