[maker-devel] maker2jbrowse implementation

[V Wong]

Hi Carson and Robert,

Thank you for your feedback on this!  Carson, could you describe the set up
a little more?  For instance, are you running the script in a specific
location in the JBrowse directory?  I seem to be running into the same
problem as Robert.

Best,
Val


On Wed, Jul 3, 2013 at 11:02 AM, Carson Holt <carsonhh at gmail.com> 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  It is very out of date.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   Of course this tutorial is also likely to be somewhat out of date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
> >> _______________________________________________ maker-devel mailing list
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> >
> >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> >>
> >>
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> >>
>
>
>
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