visualization through Trackster on local Galaxy installation
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
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:
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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 <hrh@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 ___________________________________________________________ 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:
To search Galaxy mailing lists use the unified search at:
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 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:
To search Galaxy mailing lists use the unified search at:
-- Jennifer Hillman-Jackson http://galaxyproject.org
participants (3)
-
Hans-Rudolf Hotz -
Jennifer Jackson -
Yupu Liang