Pecan.synconf

This is an example configuration file for GBrowse_syn used on WormBase. It contains information about the alignment (joining) database and the individual database for of the species in the browser.

return to GBrowse_syn

[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