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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
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