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GBrowse syn Configuration
Main Configuration File
The main configuration file specifies the alignment database, the species to be included and their corresponding configuration files and display options.
- The file ends with the extension ".synconf".
Example config file
This example contains information about the alignment (joining) database and the individual database for of the species in the browser. For details of each setting, see below.
[GENERAL] description = PECAN alignments for Caenorhabditis # The synteny database join = dbi:mysql:database=pecan;host=localhost;user=nobody # symbolic src config file (without the ".conf") Description source_map = c_elegans c_elegans "C. elegans" c_remanei c_remanei "C. remanei" c_briggsae c_briggsae "C. briggsae" c_brenneri c_brenneri "C. brenneri" c_japonica c_japonica "C. japonica" tmpimages = /gbrowse/tmp imagewidth = 800 stylesheet = /gbrowse/gbrowse.css cache time = 1 # example searches to display examples = c_elegans X:1050000..1150000 c_briggsae chrX:620000..670000 c_elegans R193.2 zoom levels = 5000 10000 25000 50000 100000 200000 400000 # species-specific databases [c_elegans] tracks = CG color = green [c_remanei] tracks = CG color = red [c_briggsae] tracks = CG color = black [c_brenneri] tracks = CG color = purple [c_japonica] tracks = CG color = blue
- Another example can be found in the GBrowse_syn_Tutorial
See above for examples.
|Option||Required option?||Default Value||Description|
|join||Yes||The database source name (DSN) for the alignment database|
|source_map||Yes|| This option maps the relationship between the species data sources, names and descriptions. See the example above.
|tmpimages||The URL for cached image and session data|
|buttons||The URL for stock GBrowse images, etc|
|stylesheet||/gbrowse/gbrowse.css||The URL for the stylesheet|
|examples||Example searches to show at the top of the page The species names used much match those used in the first column of the source_map directive.|
|zoom levels||which zoom levels will be available in the navigation menu|
|config_extension||syn|| This specifies the extension of species-specific configuration files.
|description||none||The description of the GBrowse_syn data source for public display|
|max_segment||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 take a long time to render and may even time out the web server!|
|max_span||0.3||The maximum fraction of the reference sequence size that will trigger merging of adjacent inset (aligned sequence) panels.|
|min_alignment_size||0.01||The minimum alignment size, expressed as a fraction of the total reference sequence length, that will be used to create an inset panel.|
|imagewidth||800||The width of the displayed sequence in pixels.|
|interimage_pad||5||The space between inset panels in pixels. Of course you know what the inset panels are. Of course you do!|
|vertical_pad||5||The vertical space between panels in pixels.|
|align_height||6||The height of the alignment syntenic block features in pixels.|
|max_gap||200_000||The maximum gap allowed between chained alignment features.|
|overview_ratio||0.9||The relative width of the overview panel in relation to the width of the detailed display panel.|
|overview bgcolor||gainsboro||The background color of the overview panel. Allowed values are named web colors or RGB hex codes (eg: '#FFFFFF').|
The species' configuration stanzas
- Each individual species (or equivalent) that has a configuration file specified in the source map should also have a config stanza specifying which tracks to display and the theme color for the species.
- Note that the label of each stanza must match one of those in the second column of the source_map.
[elegans_synteny] tracks = CG color = blue [briggsae_synteny] tracks = CG color = purple [remanei_synteny] tracks = CG color = black