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 <[email protected]> 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 >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ >> ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
