[maker-devel] maker2jbrowse implementation

[Robert Buels]

How does this have anything to do with CSS?  The errors Val is talking 
about are coming from the maker2jbrowse script:

ERROR: No track information for source
 >>> 'AK_assembly_datastore/22/D4/AK_contig_1/'


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/03/2013 12:02 PM, Carson Holt wrote:
> I think you may not have it set up right.  If you run the example data,
> you can then use that.  For me it populates the JSON data tracks
> information, but nothing displays.  I think the problem is with the maker
> genome.css.  It is very out of date.  I'll do some work on it and then get
> your feedback.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>
>> After looking at the maker2jbrowse source (thanks for giving me access),
>> there seems to be some kind of problem with the way maker2jbrowse is
>> parsing the MAKER datastore index, leading to the script complaining of
>> 'no track information'.
>>
>> This would probably be easier for a MAKER developer to look into.
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>> which is not backwards compatible with other Jbrowse versions), as a
>>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>>> not work with all versions).  I'm not sure if the script is currently
>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>> have it working with whatever the most current repository is if you were
>>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>    Of course this tutorial is also likely to be somewhat out of date
>>> :-( But the 2013 version is supposed to be up and running as part of
>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>> data for the tutorial, so it should be relevant to what you are doing.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Date: Tuesday, July 2, 2013 11:38 AM
>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>>> Subject: [maker-devel] maker2jbrowse implementation
>>>
>>> Hi Maker team,
>>>
>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>> server, using the -d option for the index.log file.  However, I am
>>> getting this error for each contig:
>>>
>>> ERROR: No track information for source
>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>
>>> Looking at the perl script, the file locations are getting read, but
>>> then the tracks aren't getting found in the hash of commands.
>>>
>>> Any advice for getting past this will be most appreciated.  Thank you!
>>>
>>> Best,
>>> Val
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>
>
>