Difference between revisions of "GBrowse syn Configuration"
From GMOD
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===config_extension=== | ===config_extension=== | ||
* default: 'syn'; | * 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'. | + | * 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). | * 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). | ||
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===min_alignment_size=== | ===min_alignment_size=== | ||
* default: 0.01 | * 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. | + | * The minimum alignment size, expressed as a fraction of the total referece sequence length, that will be used to create an inset panel. |
| − | + | ||
===imagewidth=== | ===imagewidth=== | ||
* default: 800 | * default: 800 | ||
* The width of the displayed seuence panels (pixels) | * The width of the displayed seuence panels (pixels) | ||
| + | ===interimage_pad=== | ||
* default: 5 | * default: 5 | ||
* The space between inset panels (pixels) | * 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') | ||
| + | |||
| − | *By default these files has the extension ".syn", but regular GBrowse configuration files (extension .conf) can also be used by changing the configuration option '' in the main config file (above) | + | *By default these files has the extension ".syn", but regular GBrowse configuration files (extension .conf) can also be used by changing the configuration option '' in the main config file (above) |
*This file is identical in structure to a normal [[CONFIGURE_HOWTO#ADDING_A_NEW_DATABASE_TO_THE_BROWSER|GBrowse configuration file]]. | *This file is identical in structure to a normal [[CONFIGURE_HOWTO#ADDING_A_NEW_DATABASE_TO_THE_BROWSER|GBrowse configuration file]]. | ||
Revision as of 12:54, 13 January 2009
Contents
Main Configuration File
Purpose
The main configuration file specifies the alignment database, the species to be included and their corresponding configuration files.
- This file ends with the extension ".synconf".
- An example of the config file for the WormBase synteny browser can be seen here.
Configurable options
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')
- By default these files has the extension ".syn", but regular GBrowse configuration files (extension .conf) can also be used by changing the configuration option in the main config file (above)
- This file is identical in structure to a normal GBrowse configuration file.
- 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 for the WormBase synteny browser can be seen here
