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 jen@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 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
Using full path in the ini file fix the problem!
Thanks, Yupu On Jan 30, 2014, at 10:21, Jennifer Jackson jen@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 jen@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 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
-- Jennifer Hillman-Jackson http://galaxyproject.org
Yupu,
Very glad! The thanks goes to Jeremy who sorted out the issue.
We had some big changes the last few release cycles, and unexpected issues popped out. It was very nice of you to not only take the time to report the problem, but to also follow up with sending feedback until resolved.
If this is not corrected soon for some reason (as it is expected to be), I will add a temporary note to the wiki instructions. But, mainling list Q & A, like this conversation, will show up in our Galaxy custom searches. So can certainly help others, just as it is, right now.
Thanks again, your patience and help confirming the work-around in a local build (one not run by a team member) are very much appreciated!
Best,
Jen Galaxy team
On 1/30/14 9:17 AM, Yupu Liang wrote:
Using full path in the ini file fix the problem!
Thanks, Yupu On Jan 30, 2014, at 10:21, Jennifer Jackson jen@bx.psu.edu wrote:
galaxy-user@lists.galaxyproject.org
-
Jennifer Jackson -
Yupu Liang