[maker-devel] maker2jbrowse

[Barry Moore]

Hi Robert,

Yes, the MAKER source code is open under either the Artistic or GNU GPL for academic use.  You can download the code here:

http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi.

Registration allows us to track unique user downloads and create cool geocoded maps for funding purposes :)

B

> From: Robert Buels <rbuels at gmail.com>
> Subject: Re: [maker-devel] maker2jbrowse implementation
> Date: July 2, 2013 11:32:40 AM MDT
> To: <maker-devel at yandell-lab.org>
> 
> 
> 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  Of course this tutorial is also likely to be somewhat out of date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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>> 
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> 
> 
> 
> 
> From: <maker-devel-request at yandell-lab.org>
> Subject: confirm 25a5d094a80beae62e51d1f0ee53d38a5d0bfacc
> Date: July 2, 2013 11:32:44 AM MDT
> 
> 
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> 

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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