Re: [Gmod-ajax] using biodb-to-json.pl on volvox_conf.json but no track was outputted

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Thanks Mitch for the detailed reply.
  Previously I thought biodb-to-json.pl will automatically treat the
first line in volvox.gff3 (ctgA example ........ Name=ctgA) as the
reference sequence similar to gbrowse so no prepare-refseqs.pl is
required when directly converting the config file. Anyway, I was wrong. 
 Just tried the 'git pull', but showed 'Failed to find a valid git
directory'. That's not important anyway.
 For other users' reference, after I used prepare-refseqs.pl and
biodb-to-json.pl. Since I used the --out parameter to specify a new
output location, I needed to manually modify the index.html file so that
it points to the correct location of refSeqs.js and trackInfo.js.

  Thank the whole jbrowse developing team for developing such a nice UI.
Hope it will continue to be successful and provide richer features and
functionalities in the soon future.

Regards,
Kenneth

-----Original Message-----
From: Mitch Skinner [mailto:mit...@be...] 
Sent: Thursday, March 18, 2010 2:48 AM
To: CHAN, KENNETH 1 [AG/7721]
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] using biodb-to-json.pl on volvox_conf.json but
no track was outputted

Did you run prepare-refseqs.pl?

Also, I think that vmware image has git installed, so it might help to 
go into
/var/www/jbrowse/
and run "git pull" to update that jbrowse installation.

Also, by default, the "data" directory is created as a subdirectory of 
the working directory that the scripts are run from, and (by default) 
the index.html file expects the "data" directory to be in the same 
directory as the index.html file.  So if you run the scripts from the 
"jbrowse" directory (i.e., if you run them like: bin/prepare-refseqs.pl)

then you can just use the defaults, otherwise use the --out parameter to

specify the location of the data directory.

Hope this helps,
Mitch

On 03/17/2010 09:26 AM, CHAN, KENNETH 1 [AG/7721] wrote:
> Hello all,
>    I downloaded the VMware ('Ending Image' in
> http://gmod.org/wiki/JBrowse_Tutorial) and tried to convert the
> configuration file (volvox_conf.json) to json. However no track was
> outputted by the following steps:
> - go to '/var/www/jbrowse/docs/tutorial/conf_files'
> - change the db_args attribute to point to the correct data directory:
> "-dir": "/var/www/jbrowse/docs/tutorial/data_files" },
> - in the same conf_files directory and type:
> ../../../bin/biodb-to-json.pl --conf volvox.json
> - it created directories 'data/tracks', but somehow nothing is in both
> dir or sub-dir.
>
> Did I do anything wrong or missed out any crucial steps? (I was
> expecting the biodb-to-json.pl will generate all tracks in the config
> file directly.)
> Thanks.
>
> Regards,
> Kenneth
>
>
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