Hi Nate,
I'm running
changeset: 12641:cab3db6e1d59
and I can see the same behaviour. The blast job is not listed under jobs
in the admin section and I can't kill it, also not via deleting the dataset.
Anything I can do to track that down?
In my case it's a large blast job with splitting
Hi Brad,
If you're using HTTP Auth, that will be the case since HTTP Auth has no notion
of sessions, the auth credentials must be provided with every request.
For a more robust solution, you probably want to use an auth filter that
creates an authentication session. Penn State uses Cosign for
Hi Peter,
This galaxy instance is connected to our SGE, and all jobs get run on it.
When we started this particular job, and it was the only job running, 4 of
the 10 tasks it was split to were able to run simultaneously, which we
viewed with qstat.
But after those four completed successfully,
Hmm.
This could be related to the problem Bjoern recently reported,
which Nate says was partly addressed in a recent fix:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-February/018367.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-February/018382.html
What version of Galaxy do you
Hmm... this is fairly odd. My first instinct would library permission
problems but this error message seems related to the target history of
the import - a much more straight forward process. I am unable to
reproduce this locally and I cannot think of any recent change that
would cause this. So my
Hi Björn,
Does stopping other, non-split jobs work correctly for you?
--nate
On Wed, Feb 26, 2014 at 7:30 AM, Björn Grüning bjoern.gruen...@gmail.comwrote:
Hi Nate,
I'm running
changeset: 12641:cab3db6e1d59
and I can see the same behaviour. The blast job is not listed under jobs
in
Hi Nate:
I'll look into an SSO situation...
I assume this works because the front end to the toolshed can check to be sure
that the admin requesting installation has an active session with the SSO
server.
?
Brad
From: Nate Coraor n...@bx.psu.edu
Sent:
Hi Nate,
sorry to bother you again, but that issue is still not fixed for me.
The following is supposed to work, or?
tool
id=toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/
destination=24_cores_24G /
tool
According to hg summary, the version is release_2013.11.04
--
Ravi Sanka
ICS Sr. Bioinformatics Engineer
J. Craig Venter Institute
301-795-7743
--
On 2/26/14 9:28 AM, Peter Cock p.j.a.c...@googlemail.com
Thanks again for the issue report. The current stable branch of
galaxy-central will now render all XML content as plain text so that
web browsers do not attempt to evaluate JavaScript contained in SVG
files. This is hopefully a short-term workaround until a SVG
sanitation can be incorporated into
Hello again Thomas,
Unfortunately I forgot about your email from last summer - which
was shortly before the GCC2013 conference where we had some
productive discussions about the BLAST+ wrappers, e.g.
http://wiki.galaxyproject.org/Events/GCC2013/BoF
Further replies in-line below...
Peter wrote:
Hi,
I need to solve a problem in Apache and could not find a solution.
So, we are using remote authentication for galaxy.myserver.edu. It is like a
basic authentication in apache.
AuthType Basic
So I want to allow machine1 to access galaxy.myserver.edu/display_application
without password.
Hi,
When I map the reads with bowtie2 to hg19.
I got the output like below and there are four display options. When I map the
reads to mm10. I got only display in “IGB Local Web option. So, how can I fix
this for mm10 or others and show all options?
101: Bowtie2 on data 4: aligned reads
91.6
Hi Björn,
Please try it without the trailing slash on the tool ID.
--nate
On Wed, Feb 26, 2014 at 11:28 AM, Björn Grüning
bjoern.gruen...@gmail.comwrote:
Hi Nate,
sorry to bother you again, but that issue is still not fixed for me.
The following is supposed to work, or?
tool
Hi Brad,
Galaxy doesn’t come with any Data Managers in the distribution, so you’ll need
to install them from a toolshed. Here is the Data Manager category with with is
currently available in the test toolshed.:
Hi,
I need to solve a problem in Apache and could not find a solution.
So, we are using remote authentication for galaxy.myserver.edu. It is like a
basic authentication in apache.
AuthType Basic
So I want to allow machine1 to access galaxy.myserver.edu/display_application
without password.
Hi Dan:
Thanks I have installed these test data managers...
I miss some of the features of the old system
e.g. lookup by name at ucsc or ncbi, automatic building of a specified set of
indices after download.
Are those cool features really gone now or did i miss something?
The second
Dear All,
I installed gatk2 from tool_shed, and see below for my
gatk2_picard_index.loc
Anyone can tell me what the mistake is? Old gatk can use this file to find
all reference genomes, but gatk2 cannot.
Fenglou
gatk2_picard_index.loc
Description: Binary data
Hi Fenglou,
which file have you edited? Under tool-data or
tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/340633249b3d/gatk2_picard_index.loc
?
Cheers,
Bjoern
Am 26.02.2014 22:37, schrieb Fenglou Mao:
Dear All,
I installed gatk2 from tool_shed, and see below for my
Thanks, edited the wrong file.
Fenglou
On 26 February 2014 16:40, Björn Grüning bjoern.gruen...@gmail.com wrote:
Hi Fenglou,
which file have you edited? Under tool-data or tool-data/
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/340633249b3d/gatk2_picard_index.loc?
Cheers,
Bjoern
Am
No problem, your welcome.
If you have any other feedback, please get in touch!
Bjoern
Am 26.02.2014 23:59, schrieb Fenglou Mao:
Thanks, edited the wrong file.
Fenglou
On 26 February 2014 16:40, Björn Grüning bjoern.gruen...@gmail.com wrote:
Hi Fenglou,
which file have you edited? Under
Hi Galaxy devs,
I had an issue recently where I must have messed up my .hgignore file or done
something terrible to my repository.
I created a bitbucket and pushed my instance to it. I then pulled that onto my
laptop and hooked it all up with Eclipse. After I was happy with my code, I
pushed
Hi Guys,
Are there anyone who is using Cistrome?
I tried to merge Cistrome's setting into our own galaxy instance. A new
entry is
# Path to the static library files for assembly, ceaslib, chromLen,
conservation, liftOver and MAT-lib
# Then in other tool configuration xml file, we can use 'from
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