Hi all,
I have a problem when I would to show the pie of krona. Galaxy show the data
but not the pie. Is it possible to show the pie in the eye mode?
I think that the jquery script which is in the output, is not read by Galaxy.
Thanks,
Clément
Dear Dannon,
Thank you for your answer, it works better now that I know the steps ID
for my workflow.
I have another question though.
The second step of my WF uses a parameter input named prefix. I really
need to specify it when I launch the WF using the API.
When i display the WF using
This might have to do with the fact that galaxy by default sanitizes
html, you can alter this behaviour with an option in universe_wsgi.ini
(but might compromise security):
# Sanitize All HTML Tool Output
# By default, all tool output served as 'text/html' will be sanitized
# thoroughly. This can
dear Galaxians,
AWS CloudFormation is now mature, and I have interest in exploiting it for
extending my local grid installation with SGE-based execute nodes with
galaxy on top.
This is something that Enis and Ryan already discussed more than 3 years
ago
Do you have Cloudman admin access on this instance?
The first thing I'd check would be http://your_instance/cloud to verify
that your instance has free disk space and to look for any errors in the
log. Then, check out the admin service list
(http://your_instance/cloud/admin)
to see if there are
Someone else might have but we have not (the same argument still holds).
Please let us know if you go down that path,
Enis
On Fri, Apr 25, 2014 at 12:35 PM, Luca Toldo lucato...@gmail.com wrote:
dear Galaxians,
AWS CloudFormation is now mature, and I have interest in exploiting it for
Hello Sarah,
This commit was made some time ago and is already in the distribution.
Are you running the latest distribution?
And you have uncommented the configuration line for this in your
universe.wgsi.ini file?
# Directory where chrom len files are kept, currently mainly used by
Hi,
has anything changed in galaxy in this regard?
Any way to modify an environment before a tools is run?
I now have a tool relying on R-devel and bioconductor devel, both of which I
can load in a module.
The tool comes from the toolshed with xml like:
command interpreter=Rscript
…
I don't
Hi Ido,
I do not get your question in all detail, but it is possible to define a
tool_dependencies.xml with a specific R version, + R libraries and use
only that specific version from your tool with requirement tags.
For an example please see various R tools from:
Dear Björn,
maybe I could change the tool, which is not mine, and which I don't want to
maintain to use a specific R-version that is already available on our cluster
and
which I can put into my path with module load R/3.1.0-devel (
http://modules.sourceforge.net/)
there even is a
Hello Ido,
Reading through your e-mail it is not clear to me whether the tool has
requirements that could be overridden. If it has package requirements
explicitly defined - those are completely configurable - you can write
arbitrary python plugins to resolve these any you wish - and (if the
On Apr 25, 2014, at 3:55 PM, John Chilton jmchil...@gmail.com wrote:
Additionally (perhaps more pertinently), I have an open pull request
(created just this week) to allow setting environment variables on a
per destination basis - this is sort of what you are getting at and
might be a better
Hi all,
I need to add a .boto file to the user that galaxy jobs get exec'ed as on
cloudman nodes. I thought it would copy over what the galaxy server has in
its home directory, but that doesn't seem to happen. How can I get things
like my .boto file to migrate over to new cloudman nodes when they
Hi Jim,
/mnt/galaxy is shared via NFS with all cluster workers -- this (or a
subdirectory) should work for you.
-Dannon
On Fri, Apr 25, 2014 at 10:56 AM, Jim McCusker
jmccus...@5amsolutions.comwrote:
Hi all,
I need to add a .boto file to the user that galaxy jobs get exec'ed as on
Hi Jun,
Galaxy does not really delete users. If you are trying to clear the user,
just change its email as an admin and register the user again with the same
address as before.
Martin
On Thu, Apr 24, 2014 at 8:56 PM, Jun Fan j@qmul.ac.uk wrote:
Hi Martin,
Thanks for the hint.
When I pass a parameter on the command line certain characters (like @) are
transformed to X+hexadecimal. Is this some sort of sanitization step? Would
using a config file (
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cconfigfile.3E_tag_set)
avoid that sort of mess?
I'm not
Hey Dannon,
I am using Galaxy (Cloudman) to analyze RNA seq data. I have a bunch of
datasets that I ran TopHat on. I am now trying to run Cufflinks etc. I used the
same data and workflow yesterday to run Cufflinks etc and that worked fine. I
used my own reference annotation (Homo sapiens hg38)
Can you attach the wrapper that produces the error? Does the dataset
have any standard error or standard output messages at the end of the
run? Also the Galaxy logs surrounding when the job runs might help
debug the problem.
On Fri, Apr 18, 2014 at 8:22 AM, Clement Lionnet
I feel like someone should respond to this but I must admin I don't
have a lot of ideas.
I assume you are able to use qsub to submit jobs from the Galaxy
server? This is worth verifying that before anything else. If that
doesn't work - the system configuration needs to be modified.
I think there
Sarah,
To my knowledge, Trackster has upgraded quite a bit since last Nov. Try
upgrading and see if that helps. Be sure to see the News Brief in the
link I sent for the full instructions linked in the first top section
titled Upgrades. Resetting metadata and other items may require
upgrades
Olivia,
Is the parameter set to 'set at runtime' when you view the workflow in the
editor? Could you send me the workflow json (just the
http://127.0.0.1:8080/api/workflows/workflow_id/ bit)?
-Dannon
On Fri, Apr 25, 2014 at 5:26 AM, Olivia Doppelt-Azeroual
olivia.dopp...@pasteur.fr wrote:
Sarah,
To my knowledge, Trackster has upgraded quite a bit since last Nov. Try
upgrading and see if that helps. Be sure to see the News Brief in the
link I sent for the full instructions linked in the first top section
titled Upgrades. Resetting metadata and other items may require
upgrades
Don't have a ton to add to Peter's suggestion I just wanted chime in
that there is definitely not some inherit Galaxy limit on the backend
for the number selections allow in a multiple input widget. I just
tried a test with 4 times this number of inputs and it worked fine.
This could well be
What are the exact conditions that will trigger autoscaling in a
galaxy/cloudman instance? I'm seeing 100% utilization on the head node but
no attempts by cloudman at spinning up new instances. What sort of state is
supposed to trigger that?
Thanks,
Jim
You can review the exact code here( see 'slow_job_turnover') :
https://bitbucket.org/galaxy/cloudman/src/7b8f04895ad309e0168cb3de66446ae20f3d8b3e/cm/services/autoscale.py?at=default
But, basically, load on any particular node isn't very useful for
autoscaling in this context because most jobs
Thanks, is the idle time configurable?
On Fri, Apr 25, 2014 at 2:43 PM, Dannon Baker dannon.ba...@gmail.comwrote:
You can review the exact code here( see 'slow_job_turnover') :
Hi Martin,
Thanks for the tip of changing email and username under SQL. I managed
that (update galaxy_user set email=’h...@haha.com’, username=’haha’ where id =
NNN) and tried to re-register with the same email. Then I got some error saying
“Internal Server Error
Galaxy was unable to
Hi all,Using two commands below, I am unable to purge deleted datasets (from a
local instance of galaxy installed on ubuntu). I have deleted some datasets
from the history panel and I want to purge only datasets not the history itself.
commands:
1. python
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