Interesting--I wonder if recent changes to the way GBrowse works broke
that? I'll have to take a look.
Scott
On Wed, 2008-02-13 at 08:30 -0800, Keith Anthony Boroevich wrote:
> Thanks Cyril, that did the trick.
>
> Cyril Pommier wrote:
> > You should try to remove do2Level, it might be that this speed
> > improvment does not work anymore
> >
> > Keith Anthony Boroevich a écrit :
> >> Hello Again,
> >>
> >> I may have spoke to soon. The problem describe below occurs whenever
> >> I search a feature that doesn't belong to the reference class. I've
> >> tried it with both features of types that are automatic classes and
> >> those that are not. If the feature name doesn't exist it provides a
> >> proper error page but if it does it throw the 'missing FROM-clause
> >> entry for table "sub_f"' error.
> >>
> >> below is the general section of my conf as Cyril requested.
> >>
> >> ----- BEGIN ----------------
> >> [GENERAL]
> >>
> >> # ---------------------------- #
> >> # --- Database Information --- #
> >> # ---------------------------- #
> >> description = S. salar Physical Map
> >> db_adaptor = Bio::DB::Das::Chado
> >> database = dbi:Pg:dbname=XXXXXX
> >> user = XXXXX
> >> pass = XXXXXX
> >>
> >> db_args = -dsn yourConnectString
> >> -enable_seqscan 0
> >> -srcfeatureslice 1
> >> -do2Level 1
> >>
> >> # Web site configuration info
> >> stylesheet = /gbrowse/gbrowse.css
> >> buttons = /gbrowse/images/buttons
> >> js = /gbrowse/js
> >> tmpimages = /gbrowse/tmp /home/asalbase/dev/htdocs/gbrowse/tmp
> >>
> >> # where to link to when user clicks in detailed view
> >> link = AUTO
> >>
> >> # what image widths to offer
> >> image widths = 450 640 800 1024
> >>
> >> # default width of detailed view (pixels)
> >> default width = 800
> >> default features = FPC_Contigs PCR_Markers BAC_Clones
> >>
> >> # The class of the feature that is used as the reference for all others
> >> reference class = ultracontig
> >> # This option controls what feature to show when the user first visits
> >> initial landmark = fps1
> >>
> >> # max default and min segment sizes for detailed view
> >> max segment = 10000000
> >> default segment = 500000
> >> min segment = 20
> >>
> >> # zoom levels
> >> zoom levels = 50 100 200 1000 2000 5000 10000 20000 50000 100000
> >> 200000 500000 1000000 2000000 5000000
> >>
> >> # whether to show the sources popup menu (0=false, 1=true; defaults
> >> to true)
> >> show sources = 1
> >>
> >> # colors of the overview, detailed map and key
> >> overview bgcolor = lightgrey
> >> detailed bgcolor = lightgoldenrodyellow
> >> key bgcolor = beige
> >>
> >> # ------------------------------ #
> >> # --- Searching The Database --- #
> >> # ------------------------------ #
> >>
> >> # "automatic" classes to try when an unqualified identifier is given
> >> automatic classes = contig BAC_cloned_genomic_insert STS
> >> instructions = "Type in the name of a contig, clone or marker."
> >> # "automatic" classes to try when an unqualified identifier is given
> >> automatic classes = contig BAC_cloned_genomic_insert STS
> >> instructions = "Type in the name of a contig, clone or marker."
> >>
> >> # ---------------------- #
> >> # --- HTML Insertion --- #
> >> # ---------------------- #
> >>
> >> # inside the <head></head> section
> >> head = <link rel="stylesheet" type="text/css"
> >> href="/css/asalbase.css" />
> >>
> >> # at the top...
> >> header =
> >> # a footer
> >> footer = <p>Footer PlaceMarker</p>
> >>
> >> # Various places where you can insert your own HTML -- see
> >> configuration docs
> >> html1 = sub { use lib '/home/asalbase/dev/perl-lib'; }
> >> html2 =
> >> html3 =
> >> html4 =
> >> html5 =
> >> html6 =
> >>
> >> -------------- END ------------------------
> >>
> >>
> >> -------------------------------------------------------------------------
> >>
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> >
> >
>
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--
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Scott Cain, Ph. D. [EMAIL PROTECTED]
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory
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