Hi Jeremy,

Which version you download, the most latest one or 
vrelease_2014.02.10--2--29ce93a13ac7?

Thank you very much.
Best,
Shu-Yi

On Mar 28, 2014, at 10:47 PM, Jeremy Goecks wrote:

> I just downloaded a fresh copy of galaxy-dist and everything worked fine with 
> Trackster. This suggests that your Galaxy installation is somehow corrupted. 
> You’ll need to rollback any changes to your repository and/or start from a 
> fresh copy.
> 
> Let us know if you need help doing this.
> 
> Best,
> J.
> 
> --
> Jeremy Goecks
> Assistant Professor of Computational Biology
> George Washington University
> 
> 
> 
> On Mar 27, 2014, at 4:28 AM, Shu-Yi Su <shu-yi...@embl.de> wrote:
> 
>> Hi Jeremy,
>> 
>> I reverted the files that I have changed, and also cleaned the cache once 
>> again.  The error messages are the same:
>> 
>> Failed to load resource: the server responded with a status of 404 (Not 
>> Found)
>> require.js:1:1910Error: Script error for: libs/backbone/backbone-relational
>> http://requirejs.org/docs/errors.html#scripterror
>> http://gbcs-dev/galaxy-dev/static/scripts/utils/galaxy.utils.jsFailed to 
>> load resource: the server responded with a status of 404 (Not Found)
>> require.js:1:1910Error: Script error for: utils/galaxy.utils
>> http://requirejs.org/docs/errors.html#scripterror
>> 
>> Thanks a lot…..
>> 
>> Best,
>> Shu-Yi
>> 
>> On Mar 27, 2014, at 12:00 AM, Jeremy Goecks wrote:
>> 
>>> The next step then is to revert all the changes that you pulled from 
>>> -central and report back the errors you’re seeing. Manually pulling 
>>> selected change sets can be problematic if you don’t get all the 
>>> dependencies.
>>> 
>>> Best,
>>> J.
>>> 
>>> --
>>> Jeremy Goecks
>>> Assistant Professor of Computational Biology
>>> George Washington University
>>> 
>>> 
>>> 
>>> On Mar 26, 2014, at 11:04 AM, Shu-Yi Su <shu-yi...@embl.de> wrote:
>>> 
>>>> Hi Jeremy,
>>>> 
>>>> I cleaned the catche on both safari and firefox, but it doesn't work. It 
>>>> still shows the same error messages.
>>>> 
>>>> Thank you very much for the help!!
>>>> 
>>>> Best,
>>>> Shu-Yi
>>>> 
>>>> On Mar 26, 2014, at 2:00 PM, Jeremy Goecks wrote:
>>>> 
>>>>> This sounds like a cache issue. Both of these scripts have been removed 
>>>>> from the distribution, so they should be absent from the distribution. 
>>>>> Can you try clearing your cache and see if that fixes the issue?
>>>>> 
>>>>> Thanks,
>>>>> J.
>>>>> 
>>>>> --
>>>>> Jeremy Goecks
>>>>> Assistant Professor of Computational Biology
>>>>> George Washington University
>>>>> 
>>>>> 
>>>>> 
>>>>> On Mar 26, 2014, at 4:39 AM, Charles Girardot <charles.girar...@embl.de> 
>>>>> wrote:
>>>>> 
>>>>>> Hi Jeremy,
>>>>>> 
>>>>>> After checking, the two js scripts are absent from the release:
>>>>>> 
>>>>>> backbone-relational.js ( static/scripts/packed/libs/backbone/ )
>>>>>> galaxy.utils.js ( static/scripts/packed/utils/ )
>>>>>> 
>>>>>> bw
>>>>>> 
>>>>>> C
>>>>>> 
>>>>>> On 25 Mar 2014, at 16:16, Shu-Yi Su wrote:
>>>>>> 
>>>>>>> Hi Jeremy,
>>>>>>> 
>>>>>>> Thank you very much for the reply.
>>>>>>> 
>>>>>>> Yes, we are running on galaxy-dist, and manually pulled to update our 
>>>>>>> installation. The release version is 
>>>>>>> vrelease_2014.02.10--2--29ce93a13ac7.
>>>>>>> I have tried safari and firefox. Both are not working.
>>>>>>> Here is the error massage from console:
>>>>>>> [Error] Failed to load resource: the server responded with a status of 
>>>>>>> 404 (Not Found) (backbone-relational.js, line 0)
>>>>>>> [Error] Failed to load resource: the server responded with a status of 
>>>>>>> 404 (Not Found) (galaxy.utils.js, line 0)
>>>>>>> [Error] Error: Script error for: libs/backbone/backbone-relational
>>>>>>> http://requirejs.org/docs/errors.html#scripterror
>>>>>>>         defaultOnError (require.js, line 1)
>>>>>>>         onError (require.js, line 1)
>>>>>>>         onScriptError (require.js, line 1)
>>>>>>> [Error] Error: Script error for: utils/galaxy.utils
>>>>>>> http://requirejs.org/docs/errors.html#scripterror
>>>>>>>         defaultOnError (require.js, line 1)
>>>>>>>         onError (require.js, line 1)
>>>>>>>         onScriptError (require.js, line 1);;;
>>>>>>> 
>>>>>>> We are also wondering if there is anything we didn't set up probably 
>>>>>>> for our universe_wsgi.ini file.
>>>>>>> 
>>>>>>> Thank you.
>>>>>>> 
>>>>>>> Best,
>>>>>>> Shu-Yi
>>>>>>> 
>>>>>>> 
>>>>>>> On Mar 25, 2014, at 4:05 PM, Jeremy Goecks wrote:
>>>>>>> 
>>>>>>>> Providing some additional information will help diagnose the problem:
>>>>>>>> 
>>>>>>>> *are you running galaxy-dist? If so, have you manually pulled and 
>>>>>>>> applied commits from galaxy-central? If so, which ones?
>>>>>>>> *which Web browser are you using?
>>>>>>>> *can you please open the JavaScript console in your browser and 
>>>>>>>> provide any errors that you see?
>>>>>>>> 
>>>>>>>> Thanks,
>>>>>>>> J.
>>>>>>>> 
>>>>>>>> --
>>>>>>>> Jeremy Goecks
>>>>>>>> Assistant Professor of Computational Biology
>>>>>>>> George Washington University
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> On Mar 24, 2014, at 11:38 AM, Shu-Yi Su <shu-yi...@embl.de> wrote:
>>>>>>>> 
>>>>>>>>> Hi all,
>>>>>>>>> 
>>>>>>>>> We have recently updated our local Galaxy installation to  
>>>>>>>>> vrelease_2014.02.10--2--29ce93a13ac7 (database version is 118). I 
>>>>>>>>> found that the Trackster is not working. I have checked the latest 
>>>>>>>>> commits related to Trackster bugs. So i have updated theses files:
>>>>>>>>> ./static/scripts/viz/trackster.js (commits date: 2014-02-28)
>>>>>>>>> ./static/scripts/viz/trackster_ui.js (commits date: 2014-02-28)
>>>>>>>>> ./static/scripts/viz/trackster/tracks.js (commits date: 2014-03-16)
>>>>>>>>> ./static/scripts/utils/utils.js (commits date: 2014-03-19)
>>>>>>>>> ./static/scripts/utils/config.js (commits date: 2014-03-15)
>>>>>>>>> 
>>>>>>>>> But, it is still not working. I have tried different format…bam, bed, 
>>>>>>>>> sam….all are not working.
>>>>>>>>> I looked into all possible files I can think about that might cause 
>>>>>>>>> the problems but still don't have any clues. 
>>>>>>>>> I also looked into the log, and there is no error, but i noticed that 
>>>>>>>>> there is difference from the log where the trackster was working in 
>>>>>>>>> previous installation.
>>>>>>>>> The log where the trackster is not working:
>>>>>>>>> 1. "GET 
>>>>>>>>> /galaxy-dev/visualization/trackster?dataset_id=f04ecb1d3d259245&hda_ldda=hda
>>>>>>>>>  
>>>>>>>>> 
>>>>>>>>> The log where the trackster is working (from the old installation):
>>>>>>>>> 1. "GET 
>>>>>>>>> /galaxy/visualization/trackster?dataset_id=5d38b380cba2f4a6&hda_ldda=hda……
>>>>>>>>> 2. "GET 
>>>>>>>>> /galaxy/api/datasets/5d38b380cba2f4a6?hda_ldda=hda&data_type=converted_datasets_state….
>>>>>>>>> 3. "GET 
>>>>>>>>> /galaxy/api/datasets/5d38b380cba2f4a6?data_type=data&chrom=chr2L…..
>>>>>>>>> 
>>>>>>>>> It looks like that the trackster in new version of Galaxy does not 
>>>>>>>>> execute the second and the third steps.
>>>>>>>>> 
>>>>>>>>> Here is the screen shot when i clicked "View in new visualization" 
>>>>>>>>> (there is nothing shown up---blank)
>>>>>>>>> 
>>>>>>>>> Any ideas or suggestions are appreciated.
>>>>>>>>> 
>>>>>>>>> Thank you very much.
>>>>>>>>> 
>>>>>>>>> Best,
>>>>>>>>> Shu-Yi
>>>>>>>>> 
>>>>>>>>> <PastedGraphic-1.tiff>
>>>>>>>>> 
>>>>>>>>> ___________________________________________________________
>>>>>>>>> Please keep all replies on the list by using "reply all"
>>>>>>>>> in your mail client.  To manage your subscriptions to this
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>>>>>>>>> 
>>>>>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>>>>> http://galaxyproject.org/search/mailinglists/
>>>>>>>> 
>>>>>>>> ___________________________________________________________
>>>>>>>> Please keep all replies on the list by using "reply all"
>>>>>>>> in your mail client.  To manage your subscriptions to this
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>>>>>>>> http://lists.bx.psu.edu/
>>>>>>>> 
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>>>>>>>> http://galaxyproject.org/search/mailinglists/
>>>>>>> 
>>>>>>> ___________________________________________________________
>>>>>>> Please keep all replies on the list by using "reply all"
>>>>>>> in your mail client.  To manage your subscriptions to this
>>>>>>> and other Galaxy lists, please use the interface at:
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>>>>>>> 
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>>>>>> 
>>>>> 
>>>>> 
>>>>> ___________________________________________________________
>>>>> Please keep all replies on the list by using "reply all"
>>>>> in your mail client.  To manage your subscriptions to this
>>>>> and other Galaxy lists, please use the interface at:
>>>>> http://lists.bx.psu.edu/
>>>>> 
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>>>> 
>>> 
>>> 
>>> ___________________________________________________________
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>> 
> 
> 
> ___________________________________________________________
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