Regarding the data input from out source

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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

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arab.conf (5K) Download Attachment
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Re: Regarding the data input from out source

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 <[hidden email]> wrote:
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

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--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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