Hi all,
We have installed a local galaxy server and we are encountering a problem when
trying to use UCSC display application on private dataset.
UCSC is giving us the following error message :
Unrecognized format line 2 of http://.../galaxy.bed
(note: chrom names are case sensitive)
Curiously,
Indeed, following error occurs:
157.193.10.150 - - [19/Mar/2013:08:30:06 +0200] GET
/visualization/trackster HTTP/1.1 200 - http://galaxy.bits.vib.be/;
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.22+ (KHTML, like Gecko)
Chromium/17.0.963.56 Chrome/17.0.963.56 Safari/535.22+
Hi, I have lost my view in UCSC link on my customtrack datatypes, I'm
not sure when this happened. External display links are still working
ok for other datatypes. I have set the genome database to hg18.
Any idea what I will need to edit to get this back?
Thanks
Shaun webb
--
The
Hi all,
I noticed today that there is a new yellow warning on the NCBI
BLAST+ repository in the main Galaxy Tool Shed,
http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
Quote:
The settings for name, version and type from a contained tool
configuration file's requirement tag does not
Hi Peter,
On Mar 19, 2013, at 7:44 AM, Peter Cock wrote:
Hi all,
I noticed today that there is a new yellow warning on the NCBI
BLAST+ repository in the main Galaxy Tool Shed,
http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
Quote:
The settings for name, version and type from
On Tue, Mar 19, 2013 at 1:15 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
You are correct. A tool dependency definition is associated with a tool via
the tool config's requirement tag set. The combination of name, version
and type is used to associated a tool with a tool dependency.
On Tue, Mar 19, 2013 at 1:43 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
Please feel free to edit the ToolConfigSyntax page if you get a chance.
Unfortunately I have my hands full with just the tool shed wiki, and it is
not possible for me to get time to keep the extensive Galaxy
Hi all,
Exporting histories fails on our server: Reason: *Error reading from
remote server.
*When looking at the logs and the system:
tail /var/log/messages
Mar 19 15:52:47 galaxy abrt[25605]: Write error: No space left on device
Mar 19 15:52:49 galaxy abrt[25605]: Error writing
Hi all,
I want to use the encode tools as random intervals in my local instance
of galaxy cistrome.
I have the xml file and the py file which can run the tool, but it required
any local data.
These data are referenced in tool-data/regions.loc but I've not found where
can I procure the bed which
Hello! Yesterday I updated the Flexbar tool definition in the Galaxy Tool Shed
repository flexbar to work with the new version 2.33 of the program. After
upload, a message indicating an internal server error showed up. Subsequently,
I retried it with a tarball which did not work out either. I
Dear Sir or Madam,
I hope this reaches you well. Unfortunately, I am still experiencing the same
problem as stated in my previous attached email. After a Galaxy-project's
moderator stopped my old runs. I was able to run 1 cufflinks set. Then any
subsequent tests are running into the same
Hi Zain,
This is in also in reply to your email this morning:
5:54 AM (US Pacific Coast Time)
[galaxy-dev] Same Problems with Galaxy-Project since 3/14/2013 update
For any jobs that may have been terminated, please re-run. As the
servers/clusters were brought back up online following the
Hi all,
Here is an update regarding the problem we are facing with Julien with our
local instance of Galaxy.
As Julien said
we are encountering a problem when trying to use UCSC display application
on private dataset.
UCSC is giving us the following error message :
Unrecognized format line 2 of
Hi,
I am sure these questions had been asked before but could not find the right
answer or did not look enough :) . I just want to add new aligner tool wrapper
into local galaxy. I used the existing wrappers (i.e bwa) as template and then
modified it accordingly.
Here are what I did:
Create
Johannes,
The internal server error you encountered has been resolved as of
9105:7b5f97700fdc.
The tool shed not letting you delete the flexbar subfolder was a result
of untracked files in the repository path. We have removed those files,
and your repository should now be correct.
On Tue, Mar 19, 2013 at 5:38 PM, Hakeem Almabrazi halmabr...@idtdna.com wrote:
Hi,
I am sure these questions had been asked before but could not find the right
answer or did not look enough J . I just want to add new aligner tool
wrapper into local galaxy. I used the existing wrappers (i.e
Hello,
I am setting up a local galaxy installation and using our local SGE
cluster to run the jobs as real users.
One of the first few tools I tested was the ncbi makebkastdb tool. When
I try to run it the history for that particular job is immediately shown
as follows:
0: (unnamed
Hello, Stephanie and Julien
What revision are you using IGBMC?
Can you clarify what you mean by a private dataset? Are non-owners
importing into a history via a shared history, or are they being passed a
direct link to the UCSC display viewer from the owner?
Thanks for the information,
Carl
Hello, Julien
Please see my reply and questions to Stephanie in her latest update.
Thanks,
Carl
On Mon, Mar 18, 2013 at 2:20 PM, Julien SEILER seil...@igbmc.fr wrote:
Hi all,
We have installed a local galaxy server and we are encountering a problem
when trying to use UCSC display
Indeed, following error occurs:
157.193.10.150 - - [19/Mar/2013:08:30:06 +0200] GET /visualization/trackster
HTTP/1.1 200 - http://galaxy.bits.vib.be/; Mozilla/5.0 (X11; Linux x86_64)
AppleWebKit/535.22+ (KHTML, like Gecko) Chromium/17.0.963.56
Chrome/17.0.963.56 Safari/535.22+
I'm unable to reproduce this behavior using a clean version of galaxy-dist. The
code (export_history.py) doesn't create any temporary files and appears to
write directly to the output file, so it seems unlikely that Galaxy is writing
anything to the root directory.
Can you provide the name of
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