[maker-devel] maker2jbrowse implementation

[Carson Holt]

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also likely to be somewhat out of date :-( But the 2013 version is supposed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>
Reply-To:  <vwong at umn.edu>
Date:  Tuesday, July 2, 2013 11:38 AM
To:  <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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