[maker-devel] maker2jbrowse implementation
V Wong
vwong at umn.edu
Mon Jul 15 11:57:30 MDT 2013
Hi Carson,
I tried running maker2jbrowse in the browser directory with existing
tracks, but the script expects to be run in the JBrowse directory and
printed this error:
FATAL: Can not find ./bin/flatfile-to-json.pl
Make sure you are running inside the JBrowse directory
Hi Robert,
I tried adding an Alignment2 track in the format of the example to the
browser with Maker tracks (those get viewed fine), but I am getting the
error "404 (Not found) when attempting to fetch ...[bam.bai file]" even
though the specified file is in that location.
Thank you both for your continued aid.
Since this is departing Maker for strictly JBrowse territory, would it be
more appropriate to move to the JBrowse list?
Best,
Val
On Thu, Jul 11, 2013 at 1:27 PM, Robert Buels <rbuels at gmail.com> wrote:
> 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<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<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<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 <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<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 <maker-devel at yandell-lab.org>>
>> >>>>><mailto:maker-devel@**yandell-lab.org<maker-devel at yandell-lab.org><mailto:
>> maker-devel at yandell-**lab.org <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<maker-devel at box290.bluehost.com>
>> <mailto:maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> >
>> >>>>><mailto:maker-devel@**box290.bluehost.com<maker-devel at box290.bluehost.com>
>>
>> <mailto:maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> >>
>> >>>>>
>> >>>>>http://box290.bluehost.**com/mailman/listinfo/maker-**
>> devel_yandell-lab.or<http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or>
>> >>>>>g
>> >>>>>
>> >>>>>
>> >>>>> ______________________________**_________________
>> >>>>> maker-devel mailing list
>> >>>>>maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> <mailto:maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> >
>> >>>>>
>> >>>>>http://box290.bluehost.**com/mailman/listinfo/maker-**
>> devel_yandell-lab.or<http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or>
>> >>>>>g
>> >>>>>
>> >>>
>> >>>
>> >>>
>> >
>> >
>>
>>
>>
>>
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