template.conf 4.7 KB

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  1. [GENERAL]
  2. description = <#gbrowse_name#>
  3. db_adaptor = Bio::DB::SeqFeature::Store
  4. db_args = -adaptor DBI::mysql
  5. -dsn dbi:mysql:database=<#database_name#>;host=localhost
  6. -user 'www-data'
  7. plugins = BatchDumper FastaDumper Submitter
  8. # Web site configuration info
  9. gbrowse root = gbrowse
  10. stylesheet = gbrowse.css
  11. buttons = images/buttons
  12. js = js
  13. tmpimages = tmp
  14. region segment = 100000
  15. # advanced features
  16. balloon tips = 1
  17. balloon style = GBox
  18. drag and drop = 1
  19. # one hour
  20. cache time = 0
  21. # where to link to when user clicks in detailed view
  22. link = AUTO
  23. # what image widths to offer
  24. image widths = 450 640 800 1024
  25. # default width of detailed view (pixels)
  26. default width = 640
  27. # max and default segment sizes for detailed view
  28. max segment = 500000
  29. default segment = 50000
  30. # zoom levels
  31. zoom levels = 50 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000
  32. # whether to show the sources popup menu (0=false, 1=true; defaults to true)
  33. show sources = 1
  34. # colors of the overview, detailed map and key
  35. overview bgcolor = #EAF3D1
  36. detailed bgcolor = #EAF3D1
  37. key bgcolor = lightgrey
  38. # color of the selection rectangle
  39. hilite fill = honeydew
  40. hilite outline = darkseagreen
  41. # examples to show in the introduction
  42. #examples = MtChr1:325500..329900 MtChr1:182000..199000 MtChr1:148000..193000 MtChr3:42058653..42059652
  43. # "automatic" classes to try when an unqualified identifier is given
  44. automatic classes = Symbol Gene Clone
  45. ### HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS ###
  46. # inside the <head></head> section
  47. head =
  48. # at the top...
  49. #header = <font color="white">Pulse Crop GBrowse</font>
  50. # a footer
  51. #footer = <hr>
  52. # <table width="100%"><TR><TD align="LEFT">
  53. # 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
  54. # mail to <a href="mailto:lacey.sanderson@usask.ca">lacey.sanderson@usask.ca</a>.
  55. # </TD></TR></table>
  56. # <hr><pre>$Id: Medicago Assembly 3.5, Pulse GBrowse v 1.0 02/02/2011 laceysanderson Exp $</pre>
  57. # Various places where you can insert your own HTML -- see configuration docs
  58. html1 =
  59. #html2 = <p align="center"><b>All features are displayed on the Medicago 3.5 chromosomes regardless of species of origin.</b></p>
  60. html3 =
  61. html4 =
  62. html5 =
  63. html6 =
  64. # Advanced feature: custom balloons
  65. custom balloons = [balloon]
  66. delayTime = 500
  67. [GBox]
  68. balloonImage = Box.png
  69. stem = 0
  70. vOffset = 20
  71. hOffset = 20
  72. padding = 1
  73. shadow = 0
  74. # Advanced feature: an example of a customized popup mentu for rubber band selection
  75. [OVERVIEW SELECT MENU]
  76. width = 100
  77. html = <table style="width:100%">
  78. <tr><th style="background:lightgrey">Overview</span></th></tr>
  79. <tr><td><span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.clearAndSubmit()">Zoom</span></td></tr>
  80. <tr><td><span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.cancelRubber()">Cancel</span></td></tr>
  81. </table>
  82. [DETAIL SELECT MENU]
  83. width = 250
  84. html = <table style="width:100%">
  85. <tr><th style="background:lightgrey;cell-padding:5">SELECTION
  86. <span style="right:0px;position:absolute;color:blue;cursor:pointer" onclick="SelectArea.prototype.cancelRubber()"> [X] </span> </th></tr>
  87. <tr><td><span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.clearAndSubmit()">Zoom in</span></td></tr>
  88. <tr><td><span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.clearAndRecenter()">Recenter on this region</span></td></tr>
  89. <tr><td onmouseup="SelectArea.prototype.cancelRubber()"><a href="?plugin=FastaDumper;plugin_action=Go;name=SELECTION" target="_BLANK">
  90. Dump selection as FASTA</a></td></tr>
  91. <tr><td onmouseup="SelectArea.prototype.cancelRubber()"><a href="?name=SELECTION;plugin=Submitter;plugin_do=Go;Submitter.target=NCBI_BLAST" target="_BLANK">
  92. Submit selection to NCBI BLAST</a></td></tr>
  93. </table>
  94. # Configuration for submitter plugin (used in above menu)
  95. [Submitter:plugin]
  96. submitter = [NCBI_BLAST]
  97. confirm = 1
  98. url = http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
  99. seq_label = QUERY
  100. PAGE = Nucleotides
  101. PROGRAM = blastn
  102. DATABASE = nr
  103. CLIENT = web
  104. CMD = put
  105. # Default glyph settings
  106. [TRACK DEFAULTS]
  107. glyph = generic
  108. height = 8
  109. bgcolor = cyan
  110. fgcolor = cyan
  111. label density = 25
  112. bump density = 100
  113. link = AUTO
  114. link_target = _blank
  115. [Genes]
  116. feature = gene
  117. glyph = transcript
  118. key = Genes