Yes I have restarted my Galaxy many times and I have also tried different 
genome build such as hg18 and experience the same problem.

Yupu
On Jan 29, 2014, at 3:32, Hans-Rudolf Hotz <h...@fmi.ch> wrote:

> Hi Yupu
> 
> 
> Just double checking: Have you restarted your Galaxy server after adding the 
> len files?
> 
> 
> Regards, Hans-Rudolf
> 
> 
> On 01/28/2014 08:12 PM, 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
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