[InterMine Dev] problem when integrate intermine and jbrowse

Pengcheng Yang yangpc at biols.ac.cn
Tue Jul 28 10:11:47 BST 2015


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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