zhxd2
/
tripal


			
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							[GENERAL]
description   = <#gbrowse_name#>
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
	      	-dsn dbi:mysql:database=<#database_name#>;host=localhost
		-user 'www-data'

plugins = BatchDumper FastaDumper Submitter

# Web site configuration info
gbrowse root = gbrowse
stylesheet   = gbrowse.css
buttons      = images/buttons
js           = js
tmpimages    = tmp

region segment = 100000

# advanced features
balloon tips    = 1
balloon style = GBox
drag and drop = 1

# one hour
cache time    = 0

# 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 = 640

# max and default segment sizes for detailed view
max segment     = 500000
default segment = 50000

# zoom levels
zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000

# 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 = #EAF3D1
detailed bgcolor = #EAF3D1
key bgcolor      = lightgrey

# color of the selection rectangle  
hilite fill    = honeydew
hilite outline = darkseagreen

# examples to show in the introduction
#examples = MtChr1:325500..329900 MtChr1:182000..199000 MtChr1:148000..193000 MtChr3:42058653..42059652

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone

### HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS ###
# inside the <head></head> section
head = 

# at the top...
#header = <font color="white">Pulse Crop GBrowse</font>

# a footer
#footer = <hr>
#	<table width="100%"><TR><TD align="LEFT">
#	For the source code for this browser, see the <a href="http://www.gmod.org">Generic Model Organism Database Project.</a>  For other questions, send
#	mail to <a href="mailto:lacey.sanderson@usask.ca">lacey.sanderson@usask.ca</a>.
#	</TD></TR></table>
#	<hr><pre>$Id: Medicago Assembly 3.5, Pulse GBrowse v 1.0 02/02/2011 laceysanderson Exp $</pre>

# Various places where you can insert your own HTML -- see configuration docs
html1 = 
#html2 = <p align="center"><b>All features are displayed on the Medicago 3.5 chromosomes regardless of species of origin.</b></p>
html3 = 
html4 = 
html5 = 
html6 = 

# Advanced feature: custom balloons
custom balloons = [balloon]
                  delayTime = 500

		  [GBox]
                  balloonImage  = Box.png
                  stem          = 0
                  vOffset       = 20
                  hOffset       = 20
                  padding       = 1
                  shadow        = 0


# Advanced feature: an example of a customized popup mentu for rubber band selection
[OVERVIEW SELECT MENU]
width = 100
html  =  <table style="width:100%"> 
         <tr><th style="background:lightgrey">Overview</span></th></tr>
         <tr><td><span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.clearAndSubmit()">Zoom</span></td></tr>
         <tr><td><span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.cancelRubber()">Cancel</span></td></tr>
        </table>


[DETAIL SELECT MENU]
width = 250
html  = <table style="width:100%">
         <tr><th style="background:lightgrey;cell-padding:5">SELECTION
             <span style="right:0px;position:absolute;color:blue;cursor:pointer" onclick="SelectArea.prototype.cancelRubber()"> [X] </span> </th></tr>
         <tr><td><span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.clearAndSubmit()">Zoom in</span></td></tr>
         <tr><td><span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.clearAndRecenter()">Recenter on this region</span></td></tr>
         <tr><td onmouseup="SelectArea.prototype.cancelRubber()"><a href="?plugin=FastaDumper;plugin_action=Go;name=SELECTION" target="_BLANK">
               Dump selection as FASTA</a></td></tr>
         <tr><td onmouseup="SelectArea.prototype.cancelRubber()"><a href="?name=SELECTION;plugin=Submitter;plugin_do=Go;Submitter.target=NCBI_BLAST" target="_BLANK">
               Submit selection to NCBI BLAST</a></td></tr>
       </table>

# Configuration for submitter plugin (used in above menu)
[Submitter:plugin]
submitter = [NCBI_BLAST]
            confirm   = 1
            url       = http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
            seq_label = QUERY
            PAGE      = Nucleotides
            PROGRAM   = blastn
            DATABASE  = nr
            CLIENT    = web
            CMD       = put


# Default glyph settings
[TRACK DEFAULTS]
glyph       = generic
height      = 8
bgcolor     = cyan
fgcolor     = cyan
label density = 25
bump density  = 100
link = AUTO
link_target = _blank

[Genes]
feature		= gene
glyph		= transcript
key		= Genes