[maker-devel] maker2jbrowse implementation

[Carson Holt]

Good to know the tutorial is up to date.  I had to make several
consecutive updates to my script about a year ago with Jbrowse updates, so
I'm glad to know I can likely just fix whatever is wrong now and that will
be good for most previous and upcoming Jbrowse version :-)

It has more to do with converting data from GFF3.  maker2jbrowse is just a
script that wraps the flatfile-to-json.pl calls together with some css
files (all included in maker tar ball - it's open source).  So if anything
changes in flatfile-to-json.pl or the expected tags in css files then
maker2jbrowse won't work (the css files are where I usually get into
trouble). I just have to figure out what the changes are and then fix
them.  I know I had to do some updates for colors in Web Apollo recently
and I imagine I can just use that as a template.

Thanks,
Carson




On 7/2/13 1:32 PM, "Robert Buels" <rbuels at gmail.com> wrote:

>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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