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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--
_____________________________
Cyril Pommier
Bioinformatic Engineer
INRA - URGI
523 place des terrasses
91034 Evry cedex
Tel.: 01-60-87-37-42
06-64-30-81-85
Fax.: 01-60-87-37-00
_____________________________
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