Difference between revisions of "GBrowse syn Configuration"
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*An example of a species config file can be seen [[briggsae.synconf|here]] | *An example of a species config file can be seen [[briggsae.synconf|here]] | ||
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+ | =Temporary workflow for sample data= | ||
+ | |||
+ | The first thing we need to do is create a mysql alignment database using the command-line incantation below: | ||
+ | |||
+ | $ mysql -u root -e 'create database rice_syntney' | ||
+ | |||
+ | Then, we will load the database. This is time-consuming, so we will use a screen session to run | ||
+ | it in the background while we turn our attention to downstream tasks | ||
+ | |||
+ | $ screen | ||
[[Category:GBrowse syn]] | [[Category:GBrowse syn]] |
Revision as of 04:47, 3 August 2009
GBrowse_syn is a synteny viewer based on GBrowse. This page describes how to configure GBrowse_syn.
Contents
- 1 Main Configuration File
- 1.1 Purpose
- 1.2 Configurable Options
- 1.2.1 join
- 1.2.2 source map
- 1.2.3 tmpimages
- 1.2.4 buttons
- 1.2.5 stylesheet
- 1.2.6 examples
- 1.2.7 zoom levels
- 1.2.8 config_extension
- 1.2.9 description
- 1.2.10 max_segment
- 1.2.11 max_span
- 1.2.12 min_alignment_size
- 1.2.13 imagewidth
- 1.2.14 interimage_pad
- 1.2.15 vertical_pad
- 1.2.16 align_height
- 1.2.17 max_gap
- 1.2.18 overview_ratio
- 1.2.19 overview bgcolor
- 2 Species Configuration File
- 3 Temporary workflow for sample data
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".
- An example of the config file for the WormBase synteny browser can be seen here.
Configurable Options
join
- Required setting
- The database source name (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 (i.e., 30%)
- 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 reference sequence length, that will be used to create an inset panel.
imagewidth
- default: 800
- The width of the displayed sequence 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)
- 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 can be seen here
Temporary workflow for sample data
The first thing we need to do is create a mysql alignment database using the command-line incantation below:
$ mysql -u root -e 'create database rice_syntney'
Then, we will load the database. This is time-consuming, so we will use a screen session to run it in the background while we turn our attention to downstream tasks
$ screen