Re: [Gmod-ajax] jbrowse issue

[sergio c. <con...@gm...>]

thank you colin, i did not have time to check the refseq issue yet, but
your answers clearly point to the issue and i hope to check this soon.
thanks!
sergio

On Mon, Apr 27, 2020 at 9:40 PM Colin <col...@gm...> wrote:

> Hi there,
>
> Were there any updates here? I think that Scott Cain pointed out basically
> the important thing which was that refSeqs.json is not loading. It is ok
> for tracks.conf not to load (it is just an extra type of configuration,
> just the same stuff that can be in trackList.json but in a different syntax)
>
> For flymine it looks like refSeqs.json loads ok, at this jbrowse URL:
>
>
> http://jbrowse.intermine.org/?data=https%3A%2F%2Fwww.flymine.org%2Fquery%2Fservice%2Fjbrowse%2Fconfig%2F7227&loc=2L%3A9405770..14108511&tracks=&highlight=
>
>
> It loads this refSeqs.json:
> https://www.flymine.org/query/service/jbrowse/config/7227/seq/refSeqs.json
>
> But for covidmine it looks for this refSeqs.json:
> https://test.intermine.org/covidmine/service/jbrowse/config/2697049/seq/refSeqs.json
>
> Which gives a 404
>
> -Colin
>
>
> On Fri, Apr 24, 2020 at 1:43 PM Scott Cain <sc...@sc...> wrote:
>
>> Hi Sergio,
>>
>> Does tracks.conf exist? JBrowse does complain if it doesn't get it, but
>> it doesn't care if it's empty, so a `touch tracks.conf` may do the trick.
>> The 404 on refSeqs.json is also a pretty big problem; is it present in the
>> seq directory?
>>
>> Scott
>>
>>
>> On Fri, Apr 24, 2020 at 9:37 AM <con...@in...> wrote:
>>
>>> dear jbrowse team,
>>> i have various (intermine) applications using jbrowse, but i cannot make
>>> one working (from the same jbrowse server).
>>> i attach a screenshot which should illustrate the problem: the
>>> tracks.conf is not beind served (trackList et al seems ok).
>>> i'm using JBrowse-1.16.6, and the setup for the various mine is
>>> hopefully the same.
>>> i'm wondering if it can be a data issue?
>>> any help/pointer would be great!
>>> thanks
>>> sergio
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

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