[Gmod-gbrowse] Regarding the data input from out source

[Nalini Kanta Choudhury]

Respected Sir,
I am Nalinikanta Choudhury. I am facing problem while
feeding data from outside. On a trail basis,i gave arabidopsis data in gff
format along with conf file.But i faced problem like conf file cann't
connect to the gff file, so the track cann't be generated.So please help me
in this regard. Also tell me how to get conf file? Shall i have to manually
make or any other process is there?
Below i attached the snapshot, conf file, gff file which were generated.So
kindly help...








*Thanks & Regard*

NaliniKanta Choudhury

IASRI,Library Avenue,
New Delhi-1100120

[Scott Cain]

Hi Nalini,

The main problem is with your configuration file. In the database and
defaults sections, you have this:

-----------------------

[scaffolds:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor dbi::mysql
-dir /var/lib/gbrowse2/databases/Arabidopsis
-dsn dbi:mysql:databases=arab;host=localhost
-gff '/var/lib/gbrowse2/databases/Arabidopsis'
search options = default +autocomplete
user = apache
pass =


# Default glyph settings
[TRACK DEFAULTS]
glyph = generic
database = annotations
height = 8
bgcolor = cyan
fgcolor = black
label density = 25
bump density = 100
show summary = 99999 # go into summary mode when zoomed out to 100k

------------------------

So you are creating a database whose configuration refers to it as
"scaffolds" (that's what the "[scaffolds:database]" part means), but in the
TRACK DEFAULTS section, you refer to a database call "annotations" which
isn't defined anywhere else. I think if you change this to scaffolds it
will probably work (or come closer to working).

A few more items:

In the database section, you have several parameters for db_args that
conflict, and I honestly don't know what GBrowse would do with it. You
have options for a directory of GFF files (-gff), for a directory
containing a set of GFF and fasta files (-dir) and a for a mysql database
(-adaptor and -dsn). Which do you actually have?

There isn't a readily available tool for creating configuration files.
WebGBrowse used to be an online tool from the University of Indiana that
would help with several aspects of creating a config, but they lost funding
for the project. People generally start with tutorial or sample configs
and modify them for their own use. I would suggest making changes in very
small increments to make sure that the intermediate steps still work.

Finally, when you write about things not work in GBrowse, it's also a good
idea to give an indication if there are any errors in the apache error log
that might point to what the problem is.

Good luck,
Scott


On Fri, Nov 6, 2015 at 4:38 PM, Nalini Kanta Choudhury <

Post by Nalini Kanta Choudhury
Respected Sir,
I am Nalinikanta Choudhury. I am facing problem while
feeding data from outside. On a trail basis,i gave arabidopsis data in gff
format along with conf file.But i faced problem like conf file cann't
connect to the gff file, so the track cann't be generated.So please help me
in this regard. Also tell me how to get conf file? Shall i have to manually
make or any other process is there?
Below i attached the snapshot, conf file, gff file which were generated.So
kindly help...
*Thanks & Regard*
NaliniKanta Choudhury
IASRI,Library Avenue,
New Delhi-1100120
------------------------------------------------------------------------------
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse