[maker-devel] maker2jbrowse implementation
Robert Buels
rbuels at gmail.com
Thu Jul 11 12:27:10 MDT 2013
These days, it's better to use direct BAM access. bam-to-json.pl still
works, but the direct BAM access is much better.
See
http://gmod.org/wiki/JBrowse_Configuration_Guide#Alignment_Tracks_.28BAM.29
Robert Buels
Lead Developer
JBrowse - http://jbrowse.org
On 07/11/2013 02:23 PM, Carson Holt wrote:
> If you have a previous Jbrowse with already populated tracks you can
> just, run maker2jbrowse in that directory instead of the new Jbrowse
> directory, then the maker features will be added there. Make a backup
> copy of the directory before you do this of course incase you need to
> roll back the changes.
>
> Alternatively you will have to add those to the new Jbrowse directory
> using bin/bam-to-json.pl and following the instructions here -->
> http://gmod.org/wiki/JBrowse_Tutorial_2012#BAM_data
>
> I guess Robert can chime in here as well, since we have now moved
> outside of MAKER scripts and fully into JBrowse.
>
> --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: Thursday, July 11, 2013 1:58 PM
> To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> Cc: Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>,
> <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>,
> Robert Buels <rbuels at gmail.com <mailto:rbuels at gmail.com>>
> Subject: Re: [maker-devel] maker2jbrowse implementation
>
> Hi Carson,
>
> Ah, great! After moving the contents of ../JBrowse/data/ to our browser
> directory, the Maker tracks are now on view.
>
> However, I'm having some trouble getting our older tracks (bam
> alignments and coverage tracks) into the same browser. Neither 1.
> copying and pasting the tracks from the previous trackList.json to the
> new one nor 2. running add-track-json.pl <http://add-track-json.pl> is
> doing the job. Is it possible to merge these tracks into one browser?
>
> Best,
> Val
>
>
> On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com
> <mailto:carsonhh at gmail.com>> wrote:
>
> 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 <mailto:vwong at umn.edu>>
> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> Date: Thursday, July 11, 2013 1:10 AM
> To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>,
> Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>
> Cc: <maker-devel at yandell-lab.org
> <mailto:maker-devel at yandell-lab.org>>, Robert Buels
> <rbuels at gmail.com <mailto: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
> <mailto: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
> <mailto: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 <mailto: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 theflatfile-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 <mailto: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> <mailto:vwong at umn.edu
> <mailto:vwong at umn.edu>>>
> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu> <mailto: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>
> >>>>><mailto: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
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> <mailto:maker-devel at box290.bluehost.com>
> >>>>><mailto: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
> <mailto:maker-devel at box290.bluehost.com>
> >>>>>
> >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
> >>>>>g
> >>>>>
> >>>
> >>>
> >>>
> >
> >
>
>
>
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