[InterMine Dev] problem when integrate intermine and jbrowse

Guillaume CORNUT guillaume.cornut at versailles.inra.fr
Tue Jul 28 11:17:39 BST 2015


It is strange that your error message says 
http://localhost:8080/malariamine/malariamine/service/jbrowse/36329/stats/global 
instead of 
http://localhost:8080/malariamine/service/jbrowse/36329/stats/global

Maybe you could get a more detailed error message in your tomcat logs.

Can you check the "webapp.baseurl" and "webapp.path" properties in your 
configuration file at ~/.intermine/malariamine.properties ?
I think they should have these values:
webapp.path=malariamine
webapp.baseurl=http://localhost:8080

Best,
Guillaume Cornut

On 28/07/2015 11:11, Pengcheng Yang wrote:
> Dear Guillaume Cornut,
>
> Great information. With your suggestion, I have loaded the data into 
> JBrowse. But there encountered an error says "error an error was 
> encountered when displaying this track .... RequestError: Unable to 
> load 
> http://localhost:8080/malariamine/malariamine/service/jbrowse/36329/stats/global 
> status: 0"
>
> my jbrowse_conf.json like this:
>
>
> {
>         "datasets": {
>                 "MalariaMine-36329": {
>                         "url": 
> "?data=http://localhost:8080/malariamine/service/jbrowse/config/36329",
>                         "name": "MalariaMine"
>                 },
>         }
>
> }
>
> best,
> Pengcheng Yang
>
> On 2015/7/28 16:49, Guillaume CORNUT wrote:
>> Hello,
>>
>> As a user of InterMine I have set up a Jbrowse integration too.
>> On my intermine the data url is actually like this: 
>> http://<HOST>/<MINE>/service/jbrowse/config/<TAXON ID>
>> So for you it should be something like: 
>> http://localhost:8080/malariamine/service/jbrowse/config/5833
>>
>> Like you said, you can use this data url on any JBrowse without 
>> configuration.
>>
>> Best,
>> Guillaume Cornut
>>
>> On 27/07/2015 09:31, Pengcheng Yang wrote:
>>> Dear InterMine developers,
>>>
>>> I have scrutinized this problem days but without any progress. Sorry 
>>> for my simple question.
>>>
>>> I have set up My InterMine data warehouse and want to visualize it 
>>> using JBrowse following the instruction: 
>>> http://intermine.readthedocs.org/en/latest/webapp/third-party-tools/jbrowse/. 
>>> From this instruction, it is possible to visualize the data in 
>>> InterMine using JBrowse without any additional configuration, like 
>>> define the json file and prepare the raw data, isn't it?
>>>
>>> In the instruction, the data url is designated by: "url": 
>>> "?data=http://www.flymine.org/query/service/jbrowse/config/7227". 
>>> However, what the value for malariamine for example, if malariamine 
>>> can be visited at http://localhost:8080/malariamine .
>>>
>>> Many thanks!
>>>
>>> Best,
>>> Pengcheng Yang
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> dev at intermine.org
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>
>

-- 
Guillaume



More information about the dev mailing list