JBrowse

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JBrowse

Delmans, Mihails
Hello,

I am trying to setup JBrowse for my mine.

1) How can I get the configuration files automatically ? I inserted the following record into my jbrowse_conf.json:

{
  "datasets": {
    "MarchantiaMine": {
      "url": "?data=http://localhost:8080/marchantiamine/service/jbrowse/1480153",
      "name": "Marchantiamine"
    }
  }
}

but when I navigate to folder containing jbrowse I get:

Could not load reference sequence definitions. RequestError: Unable to load data/seq/refSeqs.json status: 404.

Thanks,
Mihails

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Re: JBrowse

Julie Sullivan
Hi Mihails,

I'm not sure why your JBrowse isn't working, your configuration file
looks correct to me.

Can you verify that JBrowse itself is working? Can you set up the test data?

file:///home/USERNAME/JBrowse-1.11.3/docs/tutorial/index.html

Specifically:
"Now, if you can see the Volvox test data, your JBrowse is working."

That will eliminate any JBrowse issues, although the error message does
make me think it must be a data problem.

Julie

On 02/09/14 12:06, Delmans, Mihails wrote:

> Hello,
>
> I am trying to setup JBrowse for my mine.
>
> 1) How can I get the configuration files automatically ? I inserted the
> following record into my jbrowse_conf.json:
>
> {
>    "datasets": {
>      "MarchantiaMine": {
>        "url":
> "?data=http://localhost:8080/marchantiamine/service/jbrowse/1480153",
>        "name": "Marchantiamine"
>      }
>    }
> }
>
> but when I navigate to folder containing jbrowse I get:
>
> Could not load reference sequence definitions. RequestError: Unable to
> load data/seq/refSeqs.json status: 404.
>
> Thanks,
> Mihails
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

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Re: JBrowse

Alex Kalderimis-2
Hi there Mihails,

I assume you are using the latest InterMine release? I assume you are
using this section of the documentation:
 
http://intermine.readthedocs.org/en/latest/web-services/how-tos/set-up-jbrowse/?highlight=jbrowse#intermine-1-3-2-point-at-an-intermine

In which case you should just check that the
http://localhost:8080/marchantiamine/service/version resource returns 17+.

Also, your data URL should contain the config segment (see the linked
example), rather than pointing at the taxon-id directly.

All best,

Alex


On 05/09/14 11:25, Julie Sullivan wrote:

> Hi Mihails,
>
> I'm not sure why your JBrowse isn't working, your configuration file
> looks correct to me.
>
> Can you verify that JBrowse itself is working? Can you set up the test
> data?
>
> file:///home/USERNAME/JBrowse-1.11.3/docs/tutorial/index.html
>
> Specifically:
> "Now, if you can see the Volvox test data, your JBrowse is working."
>
> That will eliminate any JBrowse issues, although the error message does
> make me think it must be a data problem.
>
> Julie
>
> On 02/09/14 12:06, Delmans, Mihails wrote:
>> Hello,
>>
>> I am trying to setup JBrowse for my mine.
>>
>> 1) How can I get the configuration files automatically ? I inserted the
>> following record into my jbrowse_conf.json:
>>
>> {
>>    "datasets": {
>>      "MarchantiaMine": {
>>        "url":
>> "?data=http://localhost:8080/marchantiamine/service/jbrowse/1480153",
>>        "name": "Marchantiamine"
>>      }
>>    }
>> }
>>
>> but when I navigate to folder containing jbrowse I get:
>>
>> Could not load reference sequence definitions. RequestError: Unable to
>> load data/seq/refSeqs.json status: 404.
>>
>> Thanks,
>> Mihails
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

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