[Gmod-help] sample conf file for contig alignments?

Tue Sep 23 11:11:04 EDT 2008

Hi Scott,

Please see my config file 
(for <http://www.animalgenome.org:2358/cgi-bin/gbrowse/cattle/>http://www.animalgenome.org/cgi-bin/gbrowse/cattle/ )

---------------------------------------
[GENERAL]
description = Cattle genome browser
db_adaptor  = Bio::DB::GFF
db_args     = -adaptor DBI::mysql
              -dsn     DBI:mysql:database=gb_cattle;host=localhost
              -user apache -pass

# onload = alert('Loading ... ');doSomething('arg1','arg2')

# Web site configuration info
stylesheet  = /gbrowse/gbrowse.css
buttons     = /gbrowse/images/buttons
tmpimages   = /gbrowse/tmp

# where to link to when user clicks in detailed view
link          = AUTO

# what image widths to offer
image widths  = 450 640 800 1024

# default width of detailed view (pixels)
default width = 800
default features = Chrom8:Contigs

# max and default segment sizes for detailed view
max segment     = 500000
default segment = 50000

# zoom levels
zoom levels    = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000

# whether to show the sources popup menu (0=false, 1=true; defaults to true)
show sources   = 1

# colors of the overview, detailed map and key
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor      = beige

# examples to show in the introduction
examples = I

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone

### HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS ###
# inside the <head></head> section
head = <title>Cattle Genome Track: 8</title>

# at the top...
header = <h1>Cattle Genome Track - Chromosome 8 </h1>
footer = sub {
        my $file = "/usr/local/apache/doc/default/trailerb.tmpl";
        my ($line); my($output);
        my $thisyr = `date +"%Y"`;
        my $thisdt = `date +"%B %d, %Y"`;
          if (-e $file) {
            open(FILE,"$file");
            while ($line = <FILE>) {
              $output =~ s/\$thisyr/$thisyr/g;
              $output =~ s/\$thisdt/$thisdt/g;
              $output .= $line;
            }
          close FILE;
          return $output;
          }
        }

# Various places where you can insert your own HTML -- see configuration docs
html1 = 
html2 = 
html3 = 
html4 = 
html5 = 
html6 = 

# Default glyph settings
[TRACK DEFAULTS]
glyph       = generic
height      = 8
bgcolor     = cyan
fgcolor     = cyan
label density = 25
bump density  = 100

### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks

[Centro:overview]
feature       = CEN:sgd
bgcolor       = blue
glyph         = dot
fgcolor       = black
height        = 8
point         = 1
key           = Centromeres

[Chrom8:Contigs]
glyph       = generic
height      = 8
glyph       = dot
bgcolor     = cyan
fgcolor     = navy
label density = 25
bump density  = 100
----------------------------

Appreciate it!

Zhiliang

At 10:43 AM 9/23/2008 -0400, Scott Cain wrote:
>Hi Zhiliang,
>
>Could you send me a sample of the GFF and your config file?  I'll take
>a look and see if I can figure out what the problem is.
>
>Scott
>
>
>On Tue, Sep 23, 2008 at 1:28 AM, Zhiliang Hu <zhu at iastate.edu> wrote:
>> Thanks Scott for your quick reply.
>>
>> I feel hesitate to ask on the list because this appear to be a straight-forward problem, and maybe it's only me a slow learner.
>>
>> I have a set of cattle genome assembly files (chrNN.fa; chrNN.agp; contigs.all.fa; etc). I have created .gff files from each .agp files using a script from Justin of Elsik's group, loaded to MySQL db with the bulk loader tool, and made database connections, etc.
>>
>>  > bp_bulk_load_gff.pl -u xx -p xx -d gb_cattle chr8.gff chr8.fa
>>
>> However I simply don't see the chromosome track graph: http://www.animalgenome.org/cgi-bin/gbrowse/cattle/ - It seems to me an incomplete configuration problem (I tried existing conf files, e.g. the "Honey Bee" example is connected to this new "cattle" db).
>>
>> I may be wrong but I tried to track info flow from gff/fasta files to config but not sure:
>> how each record in the gff file can be linked to sequences or there should not be (column 9's "group" info is sufficient?)
>>
>> I have scrolled through Lincoln's tutorial and "Configuration HOWTO" but don't seem to follow (1) how each section is defined to function for, and (2) how each section is related? (seems "aggregators" contain what sub-sections to show? etc).
>>
>> I am not sure where exactly I am lost ...
>>
>> Zhiliang
>>
>>
>> At 03:45 PM 9/22/2008 -0400, Scott Cain wrote:
>>>Hi Zhiliang,
>>>
>>>I'm not really sure what you are looking for.  Is your data similar to
>>>what you might find in the tutorial?  Also, when looking for config
>>>file help, it is generally a good idea to write to the GBrowse mailing
>>>list, https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse ,
>>>because it is a well subscribed list with lots of people who know
>>>config files inside and out.
>>>
>>>Scott
>>>
>>>
>>>On Mon, Sep 22, 2008 at 3:25 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
>>>> Dear Dave or Scott,
>>>>
>>>> I have managed to load a cattle chromosome contigs (GFF) to GBrowse database (MySQL), but I don't seem to see expected contig alignments... wonder could you share an example configuration file for contig alignments? (I searched for but failed to find one :)
>>>>
>>>> Thank you,
>>>>
>>>> Zhiliang
>>
>>
>
>
>
>-- 
>------------------------------------------------------------------------
>Scott Cain, Ph. D. cain.cshl at gmail.com
>GMOD Coordinator (http://gmod.org/) 216-392-3087
>Cold Spring Harbor Laboratory