Difference between revisions of "GBrowse syn Configuration"

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* Allowed values are named web colors or RGB hex codes (eg: '#FFFFFF')
 
* Allowed values are named web colors or RGB hex codes (eg: '#FFFFFF')
  
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=Species Configuration File=
  
 
*By default these files has the extension ".syn"
 
*By default these files has the extension ".syn"

Revision as of 23:52, 13 January 2009

Main Configuration File

Purpose

The main configuration file specifies the alignment database, the species to be included and their corresponding configuration files and display options.

  • This file ends with the extension ".synconf".

Configurable Options

join

  • Required setting
  • The DSN for the alignment database
#example
join        = dbi:mysql:database=pecan;host=localhost;user=nobody

source map

  • Required setting
  • This option maps the relationship between the species data sources, names and descriptions
# example:
#                 name         conf. file          description
source_map =     elegans      elegans_synteny     "C. elegans"
                 remanei      remanei_synteny     "C. remanei"
                 briggsae     briggsae_synteny    "C. briggsae"

tmpimages

  • The URL for cached image and session data
# example
tmpimages   = /gbrowse/tmp

buttons

  • The URL for stock Gbrowse images, etc
# example
buttons       = /gbrowse/images/buttons

stylesheet

  • default: /gbrowse/gbrowse.css
  • The URL for the stylesheet

examples

  • Example searches to show at the top of the page
#example
examples = elegans X:1050000..1150000
           elegans I:10762799..10789727
           briggsae chrX:620000..670000

zoom levels

  • which zoom levels will be available in the navigation menu
zoom levels = 5000 10000 25000 50000 100000 200000 400000

config_extension

  • default: 'syn';
  • This specifies the extension of species-specific configuration files.
  • If GBrowse_syn is used with stand-alone GBrowse data sources, change this option to 'conf'.
  • To avoid confusing the configuration files parser, take care to select names for species-specific configuration files that are not similar to other file names. For example, do not use both elegans.conf (for Gbrowse) and elegans.syn (for Gbrowse_syn).

description

  • default: none
  • The description of the GBrowse_syn data source for public display

max_segment

  • default: 400_000
  • The maximum allowed segment size (sequence length) for the central reference panel
  • Take care not to set this value too high. Very large segments may cause significant network latency or even time out the web server

max_span

  • default: 0.3
  • This is an advanced option.
  • The maximum portion of the reference sequence size that will trigger merging of adjacent inset (aligned sequence) panels.

min_alignment_size

  • default: 0.01
  • The minimum alignment size, expressed as a fraction of the total referece sequence length, that will be used to create an inset panel.

imagewidth

  • default: 800
  • The width of the displayed seuence panels (pixels)

interimage_pad

  • default: 5
  • The space between inset panels (pixels)

vertical_pad

  • default: 5
  • The vertical space between panels (pixels)

align_height

  • default: 6
  • The height of the alignment syntenic block features (pixels)

max_gap

  • default: 200_000
  • This is an advanced option
  • The maximum gap allowed between chained alignment features

overview_ratio

  • default: 0.9
  • The relative width of the overview panel in relation to the width of the detailed display panel

overview bgcolor

  • default: gainsboro
  • The background color of the overview panel
  • Allowed values are named web colors or RGB hex codes (eg: '#FFFFFF')

Species Configuration File

  • By default these files has the extension ".syn"
  • Regular GBrowse configuration files (extension .conf) can also be used by changing the configuration option in the main config file (above)
  • To avoid confusing GBrowse, select names for your GBrowse_syn configuration files that are not similar to the names or regular GBrowse configuration files.
  • An example of a species config file can be seen here