/
volvox_final.conf
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/
volvox_final.conf
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[GENERAL]
description = Volvox Example Database
db_adaptor = Bio::DB::GFF
db_args = -adaptor memory
-dir $HTDOCS/gbrowse/databases/volvox
aggregators = match
BAC{left_end_read,right_end_read/BAC}
processed_transcript
coding
tprofile{tlevel}
plugins = Aligner RestrictionAnnotator
# list of tracks to turn on by default
default features = ExampleFeatures
reference class = Contig
# examples to show in the introduction
examples = ctgA
# "automatic" classes to try when an unqualified identifier is given
automatic classes = My_feature
### HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS ###
# inside the <head></head> section
head =
# at the top...
header =
# a footer
footer = <hr><pre>$Id: volvox_final.conf,v 1.5 2003-11-24 16:15:34 scottcain Exp $</pre>
# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =
html5 =
html6 =
# what image widths to offer
image widths = 450 640 800 1024
# default width of detailed view (pixels)
default width = 800
# Web site configuration info
stylesheet = /gbrowse/gbrowse.css
buttons = /gbrowse/images/buttons
tmpimages = /gbrowse/tmp
# max and default segment sizes for detailed view
max segment = 50000
default segment = 5000
# zoom levels
zoom levels = 100 200 1000 2000 5000 10000 20000 40000 50000
# colors of the overview, detailed map and key
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
########################
# Plugin configuration
########################
[Aligner:plugin]
alignable_tracks = EST
upcase_tracks = CDS Motifs
upcase_default = CDS
########################
# Default glyph settings
########################
[TRACK DEFAULTS]
glyph = generic
height = 10
bgcolor = lightgrey
fgcolor = black
font2color = blue
label density = 25
bump density = 100
# where to link to when user clicks in detailed view
link = AUTO
################## TRACK CONFIGURATION ####################
# the remainder of the sections configure individual tracks
###########################################################
[ExampleFeatures]
feature = my_feature
glyph = generic
stranded = 1
bgcolor = blue
height = 10
key = Example features
[Motifs]
feature = motif
glyph = span
height = 5
description = 1
link = http://www.google.com/search?q=$description
link_target = _blank
title = Search Google for $description.
key = Example motifs
[Alignments]
feature = match
glyph = segments
key = Example alignments
[Alignments:30000]
glyph = box
[Alignments:45000]
glyph = box
bump = 0
[Clones]
feature = BAC
glyph = segments
bgcolor = yellow
strand_arrow = 1
description = 1
key = Fingerprinted BACs
[Transcripts]
feature = processed_transcript gene
glyph = processed_transcript
bgcolor = peachpuff
description = 1
key = Protein-coding genes
[CDS]
feature = coding
glyph = cds
key = Frame usage
[EST]
feature = match:est
glyph = segments
height = 6
draw_target = 1
show_mismatch = 1
canonical_strand = 1
bgcolor = sub {
my $feature = shift;
my $name = $feature->display_name;
if ($name =~ /\.5$/) {
return 'red';
} else {
return 'orange';
}
}
group_pattern = /\.[53]$/
key = ESTs
[TransChip]
feature = tprofile
glyph = xyplot
graph_type = boxes
height = 50
min_score = 0
max_score = 1000
scale = right
key = Transcriptional Profile
[DNA]
glyph = dna
global feature = 1
height = 40
do_gc = 1
fgcolor = red
axis_color = blue
strand = both
key = DNA/GC Content
[Translation]
glyph = translation
global feature = 1
height = 40
fgcolor = purple
start_codons = 0
stop_codons = 1
translation = 6frame
key = 6-frame translation
[Motifs:overview]
feature = motif
glyph = span
height = 5
description = 0
label = 1
key = Motifs