[maker-devel] maker2jbrowse implementation

[Carson Holt]

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  It is very out of date.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   Of course this tutorial is also likely to be somewhat out of date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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