Dear Peter,
up to our galaxy admin, we make use of the Data Manager, so this seems not to
be the issue here?:
[cid:image001.jpg@01D41868.AAB17910]
Mit freundlichen Grüßen
Matthias Enders
---
GERMAN SEED
Hi All - Just a quick ask - anyone have anything BAD to say about running
Galaxy on a CENTOS 7.4/Scientific Linux with AMD EPYC chipset?
Its a bit new ... but looks good on paper and we would like to grow the Galaxy
environment here.
Thanks
Gerhard
Stellenbosch IT
Thanks for getting back to us - this was actually my guess from the
original email - that it was not a blastn error message, but a Galaxy
message before ever calling BLAST.
My guess is you are seeing this issue, or something like it, with
having to restart Galaxy to reload the *.loc files?
Dear all,
finally a restart of the container solved the issue with the database/blast.
Regarding the problem with the command line:
For other tools, the command line showed up, but not for blastn, as the wrapper
encountered the error before creating the command line (this is my
There is a setting to enable showing the command line string
and full paths on disk via the "i" icon from a history entry, see
https://docs.galaxyproject.org/en/master/admin/options.html#expose-dataset-path
# This option allows users to see the full path of datasets via the
# "View Details"
Hi all,
I have a galaxy instance running 18.05 version. I recently installed
'suite_samtools_1_2' (revision: 5b673ccc8747). When I used 'Mpileup' tool, I
ran into the below error, and the jobs fail.
Error message from UI:
This job was killed when Galaxy was restarted. Please retry the job.
Hi Matthias
If for whatever reasons the "i" (view details) icon doesn't work for
you, you can use the Galaxy Report Webapp (for docker installations see:
https://github.com/bgruening/docker-galaxy-stable#Galaxy-Report-Webapp )
as an alternative.
You can find your (failed) job via "Jobs in
Dear Galaxy Community,
is there any possibility to expose the command line call, generated within
galaxy?
We searched the net and found this discussions:
https://github.com/galaxyproject/galaxy/issues/3252
https://github.com/galaxyproject/galaxy/issues/2954
But both are on the exposure to
Am 10.07.2018 um 08:54 schrieb Van Wageningen, GERHARD [gerha...@sun.ac.za]:
So those files are "just not there" due to a faulty install?
Seems so.
You can try for hisat as well.
The questions is why :(
And the
repair is to delete the __toolname.x.x.x folders from the _conda/envs
folder
So those files are "just not there" due to a faulty install? And the repair is
to delete the __toolname.x.x.x folders from the _conda/envs folder and force
conda to reinstall them?
Where can I look for the channel priorities and is there a standard rule for
them?
Thanks for your input -
Which means that your conda envs are not what they are supposed to be.
You can fix this by removing the folder and let Galaxy re-created them,
but you should figure out why they are "empty". Maybe a wrong channel
priority or network issues during installation?
Hope that helps.
You could also
Hi - tx for (fast) reply. Ok ... with this result ...
(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
/home/.galaxy/tooldeps/_conda/envs]$ trim_galore --version
-bash: trim_galore: command not found
Environment is:
Hi,
can you do:
. /home/.galaxy/tooldeps/_conda/bin/activate
'/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
And see if you can execute trim_galore from the commandline and get the
help?
Ciao,
Bjoern
Am 10.07.2018 um 08:34 schrieb Van Wageningen, GERHARD [gerha...@sun.ac.za]:
Hi
Thanks I think that helps!
Cheers Jochen
On 09.07.2018 17:36, Martin Čech wrote:
> Another recently updated resource for uwsgi is the training slides:
> https://galaxyproject.github.io/dagobah-training/2018-gccbosc/10-uwsgi/uwsgi.html#1
>
> M.
>
> On Mon, Jul 9, 2018 at 11:31 AM Peter Briggs
>
Hi Bjoern, thanks for the pointer ... We are running the default
dependency_resolvers_conf.xml now and that, along with the symlinks hint has
helped with a lot of the tool dep. issues. But there is still a pathing issue
we are stuck on.
Take for example the trim_galore tool.
The error is
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