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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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:

http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

http://galaxyproject.org/search/mailinglists/