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 <[email protected]> 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
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--
Jennifer Hillman-Jackson
http://galaxyproject.org
--
Jennifer Hillman-Jackson
http://galaxyproject.org
___________________________________________________________
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/
