Difference between revisions of "Pecan.synconf"
From GMOD
| Line 1: | Line 1: | ||
| − | This is an example configuration file for GBrowse_syn | + | This is an example main configuration file for GBrowse_syn. |
It contains information about the alignment (joining) database and the | It contains information about the alignment (joining) database and the | ||
individual database for of the species in the browser. | individual database for of the species in the browser. | ||
| Line 6: | Line 6: | ||
<code><pre> | <code><pre> | ||
| − | [GENERAL] | + | [GENERAL] |
| − | description = PECAN alignments for Caenorhabditis | + | description = PECAN alignments for Caenorhabditis |
| − | + | ||
| − | # The synteny database | + | # The synteny database |
| − | join = dbi:mysql:database=pecan;host=localhost;user=nobody | + | join = dbi:mysql:database=pecan;host=localhost;user=nobody |
| − | + | ||
| − | # symbolic src config file (without the ".conf") Description | + | # symbolic src config file (without the ".conf") Description |
| − | source_map = c_elegans c_elegans "C. elegans" | + | source_map = c_elegans c_elegans "C. elegans" |
| − | c_remanei c_remanei "C. remanei" | + | c_remanei c_remanei "C. remanei" |
| − | c_briggsae c_briggsae "C. briggsae" | + | c_briggsae c_briggsae "C. briggsae" |
| − | c_brenneri c_brenneri "C. brenneri" | + | c_brenneri c_brenneri "C. brenneri" |
| − | c_japonica c_japonica "C. japonica" | + | c_japonica c_japonica "C. japonica" |
| − | + | ||
| − | tmpimages = /gbrowse/tmp | + | tmpimages = /gbrowse/tmp |
| − | imagewidth = 800 | + | imagewidth = 800 |
| − | stylesheet = /gbrowse/gbrowse.css | + | stylesheet = /gbrowse/gbrowse.css |
| − | cache time = 1 | + | cache time = 1 |
| − | + | ||
| − | # example searches to display | + | # example searches to display |
| − | examples = c_elegans X:1050000..1150000 | + | examples = c_elegans X:1050000..1150000 |
| − | c_briggsae chrX:620000..670000 | + | c_briggsae chrX:620000..670000 |
| − | c_elegans R193.2 | + | c_elegans R193.2 |
| − | + | ||
| − | + | ||
| − | zoom levels = 5000 10000 25000 50000 100000 200000 400000 | + | zoom levels = 5000 10000 25000 50000 100000 200000 400000 |
| − | + | ||
| − | # species-specific databases | + | # species-specific databases |
| − | [c_elegans] | + | [c_elegans] |
| − | tracks = CG | + | tracks = CG |
| − | color = green | + | color = green |
| − | + | ||
| − | [c_remanei] | + | [c_remanei] |
| − | tracks = CG | + | tracks = CG |
| − | color = red | + | color = red |
| − | + | ||
| − | [c_briggsae] | + | [c_briggsae] |
| − | tracks = CG | + | tracks = CG |
| − | color = black | + | color = black |
| − | + | ||
| − | [c_brenneri] | + | [c_brenneri] |
| − | tracks = CG | + | tracks = CG |
| − | color = purple | + | color = purple |
| − | + | ||
| − | [c_japonica] | + | [c_japonica] |
| − | tracks = CG | + | tracks = CG |
| − | color = blue | + | color = blue |
</pre></code> | </pre></code> | ||
[[Category:GBrowse syn]] | [[Category:GBrowse syn]] | ||
Revision as of 00:12, 14 January 2009
This is an example main configuration file for GBrowse_syn. It contains information about the alignment (joining) database and the individual database for of the species in the browser.
[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
