[InterMine Dev] problem when integrate intermine and jbrowse

Pengcheng Yang yangpc at biols.ac.cn
Tue Jul 28 15:43:05 BST 2015


Dear Guillaume Cornut,

Thank you very much for quickly reply and kind explanation, you have 
resolved my problem. As you suggested, I changed the webapp.baseurl and 
got the expected results.

Thank you again!

Best,
Pengcheng Yang

On 2015/7/28 18:17, Guillaume CORNUT wrote:
> 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
>>>
>>
>>
>





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