[GENERAL] description = Volvox Example Database db_adaptor = Bio::DB::GFF db_args = -adaptor memory -dir '/data/www/gbrowse/html//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 Motifs:overview TransChip:region 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 section head = # at the top... header = # a footer footer =
$Id: volvox_final_withPhylo.conf,v 1.1 2008-10-22 18:54:40 lstein Exp $
# 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 # size of the "region panel" region segment = 20000 # 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 category = Examples key = Example features [Motifs] feature = motif glyph = span height = 5 description = 1 category = Proteins key = Example motifs [Alignments] feature = match glyph = segments category = Alignments key = Example alignments [Alignments:30000] glyph = box label = 0 [Alignments:45000] glyph = box bump = 0 [Clones] feature = BAC glyph = segments bgcolor = yellow strand_arrow = 1 description = 1 category = Alignments key = Fingerprinted BACs [Transcripts] feature = processed_transcript gene glyph = processed_transcript bgcolor = peachpuff description = 1 category = Genes key = Protein-coding genes [CDS] feature = coding glyph = cds category = Genes 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$/) { return 'red'; } else { return 'orange'; } } group_pattern = /\.[53]$/ category = Alignments key = ESTs [TransChip] feature = tprofile glyph = xyplot graph_type = boxes height = 50 min_score = 0 max_score = 1000 scale = right category = Genes key = Transcriptional Profile [TransChip:region] feature = tprofile glyph = xyplot graph_type = boxes height = 50 min_score = 0 max_score = 1000 bgcolor = blue scale = right key = Profile [DNA] glyph = dna global feature = 1 height = 40 do_gc = 1 fgcolor = red axis_color = blue strand = both category = Examples key = DNA/GC Content [Translation] glyph = translation global feature = 1 height = 40 fgcolor = purple start_codons = 0 stop_codons = 1 category = Proteins translation = 6frame key = 6-frame translation [Motifs:overview] feature = motif glyph = span height = 5 description = 0 label = 1 key = Motifs [Traces] feature = trace glyph = trace fgcolor = black bgcolor = orange strand_arrow = 1 height = 6 description = 1 a_color = green c_color = blue g_color = black t_color = red trace_height = 80 trace_prefix = http://localhost/gbrowse/tutorial/data_files/ key = Traces show_border = 1 [PhyloAlignment] glyph = phylo_align global feature = 1 height = 40 draw_clado_left = 0 species_spacing = 1.2 species_spacing_score = 5 hide_label = 0 fgcolor = darkblue errcolor = red axis_color = darkorange mid_axis_color = yellow clado_bg = peachpuff bg_color = white targ_color = yellowgreen ref_color = palegoldenrod key = Phylogenetic Alignment reference = volvox #tree_step_width = 5 tree_file = /Users/mokada/development/gsoc/head/htdocs/gbrowse/databases/volvox/species.tre tree_format = newick