--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
al address: Universitätstrasse 2 / LFW B 58.1 8092 Zurich,
Switzerland Office: Eschikon 27 8315 Lindau, Switzerland Phone +41 52
354 92 06 jochen.b...@usys.ethz.ch <mailto:jochen.b...@usys.ethz.ch>
www.ap.ethz.ch
--
---
Matthias Bernt
Bioinformatics Se
in galaxy.yml
`allow_user_creation: false`
and in auth_conf
```
Challenge
True
```
The configuration worked till recently (LDAP authentication still works
according to the logs)
--
---
Matthias Bernt
Bioinformatics Service
Molekulare
, in which case you can either
activate or uninstall the repo in the admin panel -> Manage tools ->
Advanced Search -> Deactivated or Uninstalled.
Hope that helps,
Marius
On Tue, 26 Mar 2019 at 15:59, Matthias Bernt <mailto:m.be...@ufz.de>> wrote:
Dear list,
I hav
can either
activate or uninstall the repo in the admin panel -> Manage tools ->
Advanced Search -> Deactivated or Uninstalled.
Hope that helps,
Marius
On Tue, 26 Mar 2019 at 15:59, Matthias Bernt <mailto:m.be...@ufz.de>> wrote:
Dear list,
I have a problem during inst
in the DB?
Thanks in advance.
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318
Dear all,
sorry for the last post .. accident. But it actually contained an
interesting question:
What are currently good approaches for testing workflows?
Cheers and sorry again :(,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare
interessieren.
Gruesse,
Matthias
Viele Grüße, *Kristian
On 7. Jan 2019, at 17:46 , Matthias Bernt <mailto:m.be...@ufz.de>> wrote:
Hi,
wir werden versuchen zumindest den Vormittag per skype zu uebertragen.
Am besten einfach mich (mbatle) ab ca 8:45 mal anschreiben.
Gruesse,
File
"/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/galaxy/serve.py",
line 54, in _serve
raise Exception(message)
Exception: Problem running Galaxy command [].
```
Would be great to have a suggestion...
C
laxy/serve.py",
line 22, in serve
return _serve(ctx, runnables, **kwds)
File
"/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/galaxy/serve.py",
line 54, in _serve
raise Exception(message)
Exception: Problem running Galaxy c
, 19 Dec 2018 at 13:53, Matthias Bernt <mailto:m.be...@ufz.de>> wrote:
Dear list,
just tried to switch to galaxy.yml, which worked in general, but now
tools that have been installed from the TS disappeared. In the logs I
get for each tool:
```
galaxy.tools.too
here? The connection to the DB seems to be
functional, since I can see the users in the admin Panel.
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - U
the switch seems unnecessary, a multiple="true" data paramater can take
either multiple
datasets or a collection.
You are right, still you could replace the list with a paired list or
list list.
Cheers,
Matthias
--
---
Matthias Bernt
Bioi
in $input_type.input_bam:
OPERATIONS...
#end for
```
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
alaxy-dev
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
End of galaxy-dev Digest, Vol 149, Issue 3
******
--
--
what I always did.
If you use a data manager, I don't know which copy it updates -
but the merging design is meant to hide these details I suppose.
Peter
On Mon, Oct 1, 2018 at 5:56 PM Matthias Bernt wrote:
Dear list,
I still have problems to get my head around tool data. Lets consider
d
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft
failed based on the exit code.
Best,
Marius
On Mon, 27 Aug 2018 at 11:52, Matthias Bernt <mailto:m.be...@ufz.de>> wrote:
Dear list,
I'm struggling to set java options for galaxy tools. Currently I use
` in my job_conf.xml and in the
script
I explored two wa
code.
Best,
Marius
On Mon, 27 Aug 2018 at 11:52, Matthias Bernt <mailto:m.be...@ufz.de>> wrote:
Dear list,
I'm struggling to set java options for galaxy tools. Currently I use
` in my job_conf.xml and in the script
I explored two ways to set java options:
`
is overwritten .. I passing GALAXY_MEMORY_MB to
the corresponding parameter might be a solution for this tool).
Any thought or suggestions on how to set the parameters in a production
environment are very welcome.
Cheers,
Matthias
--
---
Matthias
travis.yml#L113
https://github.com/peterjc/galaxy_mira/blob/206259620376b322fc8ed99a6efdd3712f38764b/.travis.datatypes_conf.xml#L42
There may be a more elegant solution nowadays using planemo to do some
of the work.
Peter
On Thu, Aug 16, 2018 at 9:30 PM, Matthias Bernt wrote:
Dear Peter,
you ar
datatype for the folder of
> output instead?
>
> Peter
>
> On Thu, Aug 16, 2018 at 4:18 PM, Matthias Bernt wrote:
> > Hi Peter,
> >
> > I hope that subclassing simple data types will be sufficient.
> >
> > More details:
> >
> > I'm currentl
which
are available via the Tool Shed, here are two:
https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blastdb
(now also in the Galaxy core)
https://github.com/peterjc/galaxy_mira/tree/master/datatypes/mira_datatypes
Peter
On Thu, Aug 16, 2018 at 3:48 PM, Matthias Bernt wrote
I created
one, but it seems that it is ignored.
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
ELEPHONE="en_US.UTF-8"
LC_MEASUREMENT="en_US.UTF-8"
LC_IDENTIFICATION="en_US.UTF-8"
LC_ALL=
*From:* Matthias Bernt
*Sent:* 06 July 2018 10:15:12
*To:* Van Wageningen, GERHARD [gerha...@sun.ac.za]
*Cc:* galaxy-dev@lists.galaxyproject.org
*Subject:* Re:
tivate conda environment! Error was: CondaEnvironmentError:
Environment error: Cannot activate environment bash. User does not have write
access for conda symlinks.
"
Galaxy started and stopped using supervisord with config below:
--
---
Matthias B
-validate
```
but get only:
```
pykwalify.errors.RuleError: match: 'None' --> '': Path:
'/mapping/galaxy/mapping/error_email_to'>
```
Any ideas where I could start digging?
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Mole
Matthias Bernt:
Dear list,
I'm looking for some inspiration for managing my galaxy instance (with
ansible). In particular I'm looking for ansible roles to
- setup quotas
- manage the tool panel (I need to get order in the chaos)
I'm wondering how the usegalaxy instances manage this? Is there some
that I could browse?
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig
which is used by qacct.
Is there a way to determine that a job was deleted from the Galaxy job
properties? It seems that in the stop_job method of the drmaa runner
does not record anywhere that the job was deleted...
Cheers,
Matthias
--
---
Matthias
?redirect=%2F
Which is true, ie. the file/directory does not exist.
Any ideas which step I forgot during the upgrade?
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH
://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/tabular.py#L90
On Fri, Jun 1, 2018 at 10:04 AM Matthias Bernt <mailto:m.be...@ufz.de>> wrote:
Dear Dannon,
its 59 columns :( the last columns are only sometimes 0.
Is there a performance issue when rendering ht
a
table. The last bit of data in particular, when looking at the sample,
is a ton of `0` columns. Is that correct?
One more possible issue is that this is sniffed as a `scidx` file, for
me, though that's unrelated to the display problem here.
-Dannon
On Fri, Jun 1, 2018 at 9:03 AM Matthias Bernt
and data are
omitted.
Is this a bug in Galaxy, or of the data in the table?
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre
,
Matthias
On 28.05.2018 11:12, H. Rasche wrote:
Hi Matthias,
On 2018-05-28, Matthias Bernt wrote:
Hi Helena,
got it running, but I struggling with subparsers (the tools that I try to
wrap basically only uses subparsers .. a lot of them). I adapted the
example.py in your repo to include a subparser
Matthias,
check this one out: https://github.com/erasche/argparse2tool
Cheers,
Bjoern
Am 28.05.2018 um 09:43 schrieb Matthias Bernt:
Dear list,
just a question for advice: I plan to wrap a python script (with lots of
options) which uses the argparse library. I was wondering if somebody has
Cool :) Thanks.
Matthias
On 28.05.2018 09:52, Björn Grüning wrote:
Hi Matthias,
check this one out: https://github.com/erasche/argparse2tool
Cheers,
Bjoern
Am 28.05.2018 um 09:43 schrieb Matthias Bernt:
Dear list,
just a question for advice: I plan to wrap a python script (with lots
the
command line...
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig
tps://github.com/conda/conda/issues/6948#issuecomment-369360906
Cheers,
Nicola
On 25/04/18 10:44, Matthias Bernt wrote:
Hi Bjoern,
still struggling with your suggestion:
> can you make sure FASTQC gets the openjdk version from conda-forge and
> not from defaults? This will fix our one proble
defaults channel has an effect .. but still
openjdk is not installed from conda-forge (instead an ominous zulu jdk
is installed from bioconda):
fastqc: 0.11.5-1 bioconda
java-jdk: 8.0.92-1 bioconda
Any comments on this?
Best,
Matthias
Am 11.04.2018 um 14:51 schrieb Matthias Ber
be handled by the conda packages or by the
Galaxy tool.
Best,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
that both should be loaded in each job. But in which order?
I guessed that the file given in the tag is sourced in the job
submit scripts, but this seems to happen not for all jobs...?
Best,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296
/h/dropboxcom-test
Regards,
Curtis
On Jan 16, 2018, at 8:12 AM, Matthias Bernt <m.be...@ufz.de
<mailto:m.be...@ufz.de>> wrote:
Dear list and a happy new year,
does anyone has experience with upload from dropbox to galaxy (by
pasting the shared link)? I always get an empty dat
lly a real download link
but a link to a website that contains some javascript button that starts
the download...
Best,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung
when registering, but I
could not remember (and could not find a way to find this information on
the toolshed page).
Best,
Matthias
On 18 December 2017 at 10:49, Matthias Bernt <m.be...@ufz.de> wrote:
Dear peter,
thanks for your comments. I tried to update:
`planemo shed_
argeted Tool Shed.
```
Any idea?
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49
g
http://biostar.usegalaxy.org
On Thu, Dec 14, 2017 at 3:34 AM, Matthias Bernt <m.be...@ufz.de
<mailto:m.be...@ufz.de>> wrote:
Dear list,
In addition to single datasets tool file inputs allow to choose between
- multiple dataset
- dataset collection
- some tools use repeat
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz
-dev/database/tmp/tmp_uHZbW'
```
Are there any suggestions how to continue with such a behavior. The file
system on our cluster seems to be slow at the moment, could this be the
cause?
Best,
Matthias
--
---
Matthias Bernt
Bioinformatics Serv
suggests
4.2.13?
Is the successful reporting of the installation a bug?
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental
laxyproject/galaxy/issues/4767
--
-------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 4822
, if this is
the case?
Best,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig
Hi,
our galaxy is behind a firewall which seems to imply that many of the nice
possibilities to use online services which download data from galaxy do not
work, e.g. phinch or the UCSC browser.
Has anybody ideas for (or experience with) workarounds?
Maybe you can elaborate about these
cloud which we might exploit, i.e.,
upload the data to OC and modify the link.
Best,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre
ed?
Best,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +
:
line 25: IntaRNA: command not found
```
Is there a list of directories and files that I could clear to get rid
of any trace of the tool and start anew?
Best,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB
and all new packages don't have this problem.
So hopefully this PR will fix it:
https://github.com/bioconda/bioconda-recipes/pull/5912
Cheers,
bjeorn
On 31.08.2017 17:19, Matthias Bernt wrote:
Dear list,
When running rmarkdown_wgcna I get the following error in the logs:
PaddingError
this helps.
Thanks again.
On Mon, Aug 28, 2017 at 4:23 AM, Matthias Bernt <m.be...@ufz.de
<mailto:m.be...@ufz.de>> wrote:
Hi Sam,
thanks for the answer. So far I have not configured anything, I was
hoping that it works out of the box :).
Could you point me to some documen
Any ideas?
Best,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Ph
Dear ...,
what are the file permissions for the file and the folder?
Is the drmaa_external_runner.py python script run with sudo?
Which release/branch are you on?
Best,
Matthias
We are setting up run as real user but have run into a strange issue.
When the drmaa external script is called
to Charts or the regular Galaxy
visualization framework? If it is the latter please make sure that you
correctly specified the datatype in your XML file. Your visualization
should than appear in the drop-down list in the history.
Thanks,
Sam
On Fri, Aug 25, 2017 at 5:25 AM, Matthias Bernt
of the GTN.
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
appears
in the main toolshed.
- I guess its not a good idea (in general) to provide tools from the
testtoolshed in a prodiction instance?
Best,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für
suspiciously like a bug that Matthias Bernt has fixed on the
development branch a while back.
I have backported this to Galaxy release 17.01 and release 17.05.
If you update your galaxy branch to the latest commit it should work (or
you should receive a more instructive error message).
Hope
/178e00cf12d7
doesn't use a Python wrapper. The development repository is at
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms
Cheers,
Nicola
On 10/08/17 14:03, Matthias Bernt wrote:
Hi,
I got an error from OpenMS which seems to be related to python3:
Fatal error: Exit code
option [shuffle] in node [at 0x2b96a3b1c048>]
Any ideas?
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research G
ging
Best,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
S
le destinations,
eg by adding it to the instead of to ?
Cheers,
Matthias
On 18.07.2017 17:14, Matthias Bernt wrote:
Dear dev-list,
again some problems with software in galaxy: I can not get numpy to
install.
Here is the excerpt from the logs:
Successfully downloaded from url:
https://dep
ot; which gives me currently a numpy
error:
Traceback (most recent call last): File
"/gpfs1/data/galaxy_server/galaxy/tools/stats/grouping.py", line 15, in
import numpy ImportError: No module named numpy
Thanks a lot.
Cheers,
Matthias
--
-
.
Peter
On Wed, Jul 12, 2017 at 3:55 PM, Matthias Bernt <m.be...@ufz.de> wrote:
Hi Peter,
I just call planemo l sleepwaste.xml
Best,
Matthias
On 12.07.2017 16:54, Peter Cock wrote:
How are you running planemo lint - in particular is it set
to fail if there are any warnings present
inting
The test of the tool are all successful. Any ideas what is wrong?
Once the problems are solved, would such a tool also be useful in the
toolshed?
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Z
are all successful. Any ideas what is wrong?
Once the problems are solved, would such a tool also be useful in the
toolshed?
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für
e tools (upload, ucsc, etc.) on the cluster (doing so
is highly recommended), set new_file_path in galaxy.ini to a directory
somewhere in your shared filesystem:
"""
Cheers,
Matthias
On 10.07.2017 11:11, Matthias Bernt wrote:
Dear Peter,
my job_conf.xml is attached.
Best,
actually informative.
Today's Topics:
1. Re: any introduce for how Mako and JavaScript work ingalaxy?
(Daniel Blankenberg)
2. Re: ustacks - bad interpreter (Björn Grüning)
3. Re: Improved DRMAAJobRunner (Peter van Heusden) (Matthias Bernt)
4. Re: Improved DRMAAJobRunne
Hi Peter,
> Code looks interesting. This is for Univa Grid Engine?
In its current state its tailored for the Univa Grid Engine. But the drmaa
library code that is based on job_info() and wait() should run on all grid
engines.
For the command line based code changes might be necessary for the
/galaxy-dev/database/tmp/ are not changed. Any
idea what needs to be changed to get this running?
Best,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz
Hi Jelle,
I just (in this very moment) solved the "option error" issue for our
galaxy installation.
see my comment on the first issue mentioned by john:
https://github.com/galaxyproject/galaxy/issues/3178#issuecomment-306538866
Maybe you do not need to compile everything from source (as I
this helps.
-John
On Thu, Jun 15, 2017 at 10:37 AM, Matthias Bernt <m.be...@ufz.de> wrote:
Dear list,
I was thinking about implementing the job resubmission feature for drmaa.
I hope that I can simplify the job configuration for our installation (and
probably others as well) by escalating t
ing the python library at all, but using
system calls to qsub, qkill, qacct, etc? Any opinions on this idea?
I guess your reaper could be of interest also for others. Is this
available somewhere?
Best,
Matthias
--nate
On Thu, Jun 15, 2017 at 10:27 AM, Matthias Bernt <m.be...@ufz.de
&
Dear list,
I was thinking about implementing the job resubmission feature for drmaa.
I hope that I can simplify the job configuration for our installation
(and probably others as well) by escalating through different queues (or
ressource limits). Thereby I hope to reduce the number of special
Dear list,
I have two question for all DRMAA users. Here is the first one.
I was checking how our queuing system (univa GridEngine) and Galaxy
react if jobs are submitted that exceed run time or memory limits.
I found out that the python drmaa library cannot query the job status
after the
.
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49
Galaxy the real username, maybe we can avoid having to setup
usern...@example.org aliases and insisting our users do that for
logging into Galaxy.
Hopefully some other SGE users can comment on how they got the
run-as-user system working for them?
Peter
On Mon, Apr 10, 2017 at 3:43 PM, Matthias Bernt
,
Matthias
On 18.05.2017 17:09, Björn Grüning wrote:
Hi Matthias,
is there any chance you can upgrade your Galaxy and enable conda packages?
This would make your life so much easier :)
Cheers,
Bjoern
Am 18.05.2017 um 16:28 schrieb Matthias Bernt:
Hi Bjoern,
thanks for the explanation. T
have been working on github :(
Ciao,
Bjoern
Am 17.05.2017 um 17:04 schrieb Matthias Bernt:
Dear galaxy-dev list,
I have problems to install package_openbabel. The problem seems to be
that cmake is not found during installation.
The documentation also states that: "Compiling Open
Dear galaxy-dev list,
I have problems to install package_openbabel. The problem seems to be
that cmake is not found during installation.
The documentation also states that: "Compiling OpenBabel requires g++
and CMake 2.4+"
My question is: Does this refer to cmake installed on the system or
:
That's a little weird, I don't think relying on the system's
LD_LIBRARY_PATH is good practice.
Maybe you could try what was suggested in the last answer
here:
https://serverfault.com/questions/372987/centos-usr-local-lib-system-wide-ld-library-path.
On 19 April 2017 at 17:57, Matthias Bernt <m
The line removal procedure seems to be quite
complicated in an automated ansible installation which I try to achieve.
Cheers,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH
1.67 at the time
of writing... it looks like we'll need to add a couple more legacy packages.
Peter
On Wed, Apr 19, 2017 at 12:01 PM, Matthias Bernt <m.be...@ufz.de> wrote:
Dear Peter,
thanks for the info. Would be great to get the update, but since I have a
method that is working for the
to BLAST+ 2.5.0 via either bioconda or the older
legacy Tool Shed.
I can try to update blast_rbh next, which may solve this by
letting you use bioconda.
Peter
On Wed, Apr 19, 2017 at 11:52 AM, Matthias Bernt <m.be...@ufz.de> wrote:
Dear Marius,
thanks again for the help. I'm trying to i
ius
On 18 April 2017 at 19:03, Matthias Bernt <m.be...@ufz.de
<mailto:m.be...@ufz.de>> wrote:
Dear list,
again me :( stumbling from problem to problem ...
I got compilation errors when installing
package_atlas_3_10 Revision: 98c017ec230d
I tried with gcc 4x and
No such file or directory
Make.top:329: warning: overriding commands for target `/AtlasTest'
Make.top:80: warning: ignoring old commands for target `/AtlasTest'
make[1]: *** No rule to make target `Make.inc'. Stop.
make: *** [build] Error 2
--
---
Matthia
s_open context=self._context) File
"/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py",
line 1198, in do_open raise URLError(err) urllib2.URLError: |
Hope that helps,
Marius
On 18 April 2017 at 17:13, Matthias Bernt <m.be...@ufz.de
1c5d2070513e_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F')
wsgi process: 'Multithreaded'
----
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmh
h-Univa-Grid-Engine-UGE-instead-of-SGE-tt4657848.html#a4657952
Does anyone has suggestions for me?
Best regards,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
this
script sudo callable? Or where could I invoke a wrapper for sudo chown
in the galaxy code?
Thanks a lot.
Best regards,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH
wrote:
This may depend on the cluster setup, and how Galaxy accesses it.
What are you using?
We use SGE (actually Univa Grid Engine) via DRMAA, and had to setup
usern...@example.org email aliases just for this.
Peter
On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt <m.be...@ufz.de> wrote:
,
Matthias
--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de,
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