Using full path in the ini file fix the problem!

Thanks,
Yupu
On Jan 30, 2014, at 10:21, Jennifer Jackson <j...@bx.psu.edu> wrote:

> Hi Yupu,
> 
> I'm sorry, I mixed up the processing for custom builds with the processing 
> for installed builds in my initial reply. A .2bit & .len file are appropriate 
> for what you are doing - and the wiki instructions are accurate.
> 
> Still, I double checked with Jeremy, the scientist that developed the tool, 
> about your issue. He found that the full path to the .len file needs to be 
> specified right now in order for installed builds to function correctly.
> 
> This deviates from the wiki instructions, but we consider this a bug and plan 
> to correct it in the next release.
> 
> Please try using the full path and let us know how that works out,
> 
> Jen
> Galaxy team
> 
> On 1/29/14 11:54 AM, Yupu Liang wrote:
>> Dear Jennifer:
>> 
>> Hi, I did put 2bit file as suggested by 
>> https://wiki.galaxyproject.org/Visualization%20Setup.
>> 
>> Should I get rid of the len file?  and I assume I will also need to take off 
>> the len_file_path out of the universe_wsgi.ini file.
>> 
>> In term of using .fasta file. I have them and I am not clear where I should 
>> put them for visualization purpose and also what adjustment i need to make 
>> in the ini file. Any help would be appreciated and I am really excited about 
>> doing all the visualization within Galaxy. I think the biologists would 
>> really love these features.
>> 
>> Thanks a lot,
>> Yupu
>> 
>> 
>> 
>> 
>> On Jan 29, 2014, at 14:21, Jennifer Jackson <j...@bx.psu.edu> wrote:
>> 
>>> Hello Yupu,
>>> 
>>> Using a .len file is problematic at this time. In the upcoming release this 
>>> will be corrected. Using a .fasta file is the solution. In many cases, 
>>> using a .fasta file can be preferred as it will include the reference 
>>> genome sequence in the visualization, but the choice is yours, once the 
>>> correction is released to the distribution.
>>> 
>>> More about this is in a recent post from Jeremy:
>>> http://lists.bx.psu.edu/pipermail/galaxy-user/2014-January/007106.html
>>> 
>>> Our apologies for the confusion this caused. The advice from Hans-Rudolf is 
>>> under normal circumstances the best first-pass route for troubleshooting, 
>>> and you will want to restart after using the fasta method as well.
>>> 
>>> Best,
>>> 
>>> Jen
>>> Galaxy team
>>> 
>>> On 1/28/14 11:12 AM, Yupu Liang wrote:
>>>> Hi,
>>>> 
>>>> I am trying to set up the visualization functionality on our local Galaxy 
>>>> installation. I followed the instructions on  
>>>> https://wiki.galaxyproject.org/Visualization%20Setup
>>>> 
>>>> And here is the list of len files:
>>>> ls -l tool-data/shared/ucsc/chrom/
>>>> total 200
>>>> -rw-rw-r-- 1 galaxy galaxy    10 Jan 27 15:13 centromeres1.len
>>>> -rw-rw-r-- 1 galaxy galaxy   821 Jan 27 15:13 hg15.len
>>>> -rw-rw-r-- 1 galaxy galaxy   713 Jan 27 15:13 hg16.len
>>>> -rw-rw-r-- 1 galaxy galaxy   792 Jan 27 15:13 hg17.len
>>>> -rw-rw-r-- 1 galaxy galaxy   855 Jan 27 15:13 hg18.len
>>>> -rw-rw-r-- 1 galaxy galaxy   202 Jan 27 15:13 hg19Haps.len
>>>> -rwxr-xr-x 1 galaxy galaxy  1971 Jan 27 15:13 hg19.len
>>>> -rw-rw-r-- 1 galaxy galaxy    67 Jan 27 15:13 hg19LggInv.len
>>>> -rw-rw-r-- 1 galaxy galaxy  4516 Jan 27 15:13 hg19Patch10.len
>>>> -rw-rw-r-- 1 galaxy galaxy  1983 Jan 27 15:13 hg19Patch2.len
>>>> -rw-rw-r-- 1 galaxy galaxy  2844 Jan 27 15:13 hg19Patch5.len
>>>> -rw-rw-r-- 1 galaxy galaxy  3879 Jan 27 15:13 hg19Patch9.len
>>>> -rw-rw-r-- 1 galaxy galaxy 11672 Jan 27 15:13 hg38.len
>>>> -rw-rw-r-- 1 galaxy galaxy    67 Jan 27 15:13 hlaRef1.len
>>>> -rw-rw-r-- 1 galaxy galaxy    67 Jan 27 15:13 hlaRef2.len
>>>> -rw-rw-r-- 1 galaxy galaxy    67 Jan 27 15:13 hlaRef3.len
>>>> -rw-rw-r-- 1 galaxy galaxy    67 Jan 27 15:13 repBase0.len
>>>> -rw-rw-r-- 1 galaxy galaxy    67 Jan 27 15:13 repBase1.len
>>>> -rw-rw-r-- 1 galaxy galaxy 12697 Jan 27 15:13 repeats2.len
>>>> -rw-rw-r-- 1 galaxy galaxy    67 Jan 27 15:13 simHuman.len
>>>> -rw-rw-r-- 1 galaxy galaxy    67 Jan 27 15:13 simHumanMammal.len
>>>> -rw-rw-r-- 1 galaxy galaxy   362 Jan 27 15:13 venter1.len
>>>> 
>>>> 
>>>> When I test the visualization through Trackster. I got the following error 
>>>> after seeing a message saying "preparing the data, this can take a 
>>>> while……":
>>>> 
>>>> Error: The requested genome file (tool-data/shared/ucsc/chrom/hg18.len) 
>>>> could not be opened. Exiting!
>>>> sort: write failed: standard output: Broken pipe
>>>> sort: write error
>>>> Couldn't open tool-data/shared/ucsc/chrom/hg18.len , No such file or 
>>>> directory.
>>>> 
>>>> 
>>>> It seems something else failed in the middle of visualization as I do have 
>>>> the hg18.len under the default path with the global reading permission……..
>>>> 
>>>> Does anybody have similar experience? Is there is way for me to debug?
>>>> 
>>>> Best,
>>>> Yupu
>>>> ___________________________________________________________
>>>> The Galaxy User list should be used for the discussion of
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>>>> 
>>> -- 
>>> Jennifer Hillman-Jackson
>>> http://galaxyproject.org
>>> 
>> 
> 
> -- 
> Jennifer Hillman-Jackson
> http://galaxyproject.org
> 


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