[maker-devel] maker2jbrowse implementation

[Robert Buels]

One of my objectives has been maintaining complete backward 
compatibility with data formatted from JBrowse 1.2.1 onward.  I add 
capabilities, and the look and feel of the browser improves, but you can 
still view data in it that was formatted with JBrowse 1.2.1 (released 
March 17, 2011).

I would try to have a look at the maker2jbrowse implementation to 
troubleshoot further, but your source code doesn't seem to be public. 
Or at least the link to the source browser on the GMOD wiki page 
(http://gmod.org/wiki/MAKER#MAKER_Development) doesn't work, and I can't 
find any kind of source code links under 
http://www.yandell-lab.org/software/maker.html.  Is the MAKER source 
code actually open?

Regarding the 2012 tutorial, the directions in the 2012 tutorial should 
still work, since I have been keeping backward compatibility with the 
scripts also.

Val, Carson, could you elaborate with details on the backward 
compatibility problems you're seeing?  Or could you give me access to 
the maker2jbrowse source code?


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   Of course this tutorial is also likely to be somewhat out of date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