Fwd: Fw: [DAS] LDAS web browser connection setup

[Lincoln Stein]

It shouldn't be necessary to use Bio::DB::Fasta any longer.  The newer 
versions of Bio::DB::GFF load the DNA into the relational database as well as 
the features.  You can leave the fasta= option blank.

Lincoln

On Sunday 21 July 2002 10:13 am, DOBBO@THEVILLAS.ECLIPSE.CO.UK wrote:
> Hi,
> it appears to be the case that I had something wrong
> with my Bio::DB::Fasta module that had slipped through
> the net (didn't notice on initial scans of the apache
> logs, thought the log was spitting out a Bio::DB::GFF
> error). The LDAS setup is fine
>
> bioperl 'make test' produced the following
>
> t/DBFasta...........AnyDBM_File doesn't define an
> EXISTS method at Bio/DB/Fasta.pm line 789
> indexing was interrupted, so
> unlinking ./t/data/dbfa/directory.index at
> Bio/DB/Fasta.pm line 948.
> t/DBFasta...........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-11
>         Failed 11/11 tests, 0.00% okay
>
> Thanks
> Rich
>
> >Is there an error in the server error log?  The most
> >common problem is a
> >password error in the config file.  Early versions of
> >the Bioperl
> >Bio::DB::GFF module did not handle username password
> >right, but this was
> >fixed before the 1.0 release.
>
> Lincoln
>
> On Friday 19 July 2002 05:31 am,
>
> dobbo@thevillas.eclipse.co.uk wrote:
> >> Hello,
> >>
> >> When I do an 'entry_points' query with my test
>
> database,
>
> >> dicty, I get the
> >> following output returned to my web browser:
> >>
> >>
> >>  Could not open database
> >>
> >> The browser returns the relevant entry from the
> >> dicty.conf file when viewing the dsn's.
> >> I'm able to use ldasdump.pl to query my test
>
> database.
>
> >> I'm also able to
> >> log in as the user 'root' and do a query using mysql.
> >>
> >> Does anyone have any suggestions on how to debug my
> >> installation?
> >>
> >> Here is the DATA SOURCE portion of my dicty.conf file
> >> that is in the
> >> das.conf subdirectory of the Apache conf directory.
> >>
> >> [DATA SOURCE]
> >> description = Test annotations
> >> adaptor     = dbi::mysqlopt
> >> mapmaster   = http://192.168.1.110/cgi-bin/das/dicty
> >> database    = dbi:mysql:database=dicty;host=localhost
> >> fasta_files = /var/annotation/dna
> >> user        = root
> >> passwd      = xxxxxxx
> >>
> >> I noticed when searching the archives somebody
>
> reported
>
> >> the same error way back in December. I pressume the
>
> fix
>
> >> is now in the 1.06 release?
> >>
> >> Any help would be greatly appreciated,
> >>
> >> Rich
> >>
> >>
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