[maker-devel] maker2jbrowse implementation

Carson Holt carsonhh at gmail.com
Thu Jul 11 05:44:07 MDT 2013 

You next put the entire JBrowse directory into the /var/www/html/ directory
or wherever you have apache set up to load from (if it's not already there).
Then it will be accessible as a webpage (browser is inside the JBrowse
directory).

Example /var/www/html/Jbrowse/
Webpage --> http://localhost/Jbrowse/

--Carson

From:  V Wong <vwong at umn.edu>
Reply-To:  <vwong at umn.edu>
Date:  Thursday, July 11, 2013 1:10 AM
To:  Carson Holt <carsonhh at gmail.com>, Ignazio Carbone <icarbon at ncsu.edu>
Cc:  <maker-devel at yandell-lab.org>, Robert Buels <rbuels at gmail.com>
Subject:  Re: [maker-devel] maker2jbrowse implementation

Hi Carson,

Thanks!  I followed your instructions, and maker2jbrowse, and it
successfully populated the ../JBrowse/data/tracks directory with
RepeatMasker, Augustus, and GeneMark predictions.

I'm not entirely sure how to get these numerous tracks into the browser, but
that may be something to work out with JBrowse rather than Maker.

Best,
Val


On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:
> Hi Val,
> 
> I've attached new files for you to test.  These will be bundled in the
> next maker release pending successful tests (~ 1 week).
> 
> Instructions:
> 1. Place maker2jbrowse in your .../maker/bin/ directory and
> .../maker/src/bin/ directory (this is just to ensure you don't
> accidentally overwrite it if you reinstall at any time).
> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
> 3. You must be in the jbrowse installation directory when running
> maker2jbrowse.  Run the script with the -d flag and the datastore index
> file.
> 
> This new version will assign colors by copying maker.css to the jbrowse
> installation as apposed to replacing the genome.css file, and it will also
> edit the genome.css file to add the import call for maker.css.  In
> addition I have updated command line flags in the wrapper to do what is
> currently expected by flatfile-to-json.pl <http://flatfile-to-json.pl> .
> 
> Could you test it out and let me know how it goes.
> 
> Thanks,
> Carson
> 
> 
> 
> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
> 
>> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>> >documentation had you modify the genome.css file to create your own
>> >tracks.  Version 1.2.1 looks like it is the last version where the
>> >genome.css file that maker provided works. I can still get simple test
>> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>> >But I need to fix some things, because they are all indistinguishable from
>> >each other (so it is not the desired behavior).
>> >
>> >Indepent of that issue though, to regenerate the original error, I do the
>> >following -->
>> >    maker2jbrowse
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >    ERROR: No track information for source
>> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>> >
>> >Basically you are missing the '-d' flag (whiteout that the script is
>> >expecting a list of GFF3 files).
>> >
>> >So this works -->
>> >    maker2jbrowse -d
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >
>> >
>> >Of course all tracks look the same though per the original issue I
>> >mentioned.
>> >
>> >Thanks,
>> >Carson
>> >
>> >
>> >
>> >Some versions of Jbrowse still load fine with the script as is Jbrowse
>> >1.3,
>> >
>> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>> >
>>> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>>> >>you're doing with that, but it appears to be a fork of a very old
>>> >>JBrowse main css file.  If that's overriding or being copied over the
>>> >>JBrowse released CSS, it will break pretty much everything.  It would be
>>> >>like me randomly replacing one of MAKER's Perl modules with my own old
>>> >>forked copy.
>>> >>
>>> >>If what you're trying to accomplish is to add some custom styles, the
>>> >>best way to do that would be to do one of:
>>> >>
>>> >>* add just your custom feature styles on the flatfile-to-json.pl
>>> <http://flatfile-to-json.pl>  command
>>> >>line
>>> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>>> >>   JBrowse trackList.json someplace in the workflow (easy to add
>>> >>   things to JSON files with JSON.pm) that loads your custom CSS
>>> >>   (containing only your custom feature styles!)
>>> >>* add all of the custom styles to the trackList.json as a
>>> >>   string: "css": "string { of: lots and lots of; css: properties; }"
>>> >>
>>> >>
>>> >>Robert Buels
>>> >>Lead Developer
>>> >>JBrowse - http://jbrowse.org
>>> >>
>>> >>On 07/03/2013 12:02 PM, Carson Holt 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
>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>> >>>>><mailto:maker-devel at box290.bluehost.com>
>>>>>> >>>>>
>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> >>>>>g
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>> _______________________________________________
>>>>>> >>>>> maker-devel mailing list
>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>> >>>>>
>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> >>>>>g
>>>>>> >>>>>
>>>> >>>
>>>> >>>
>>>> >>>
>> >
>> >
> 



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