our galaxy runs jobs as real user and I get the following error for
Failed to activate conda environment! Error was: CondaEnvironmentError:
Environment error: Cannot activate environment bash. User does not have
write access for conda symlinks. Fatal error: Exit code 1 ()
Does anyone have an idea where I could start digging? My workaround (run
the tool once as galaxy user) is to time consuming since I have to
restart galaxy 2x.
Thanks a lot.
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,
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
I am pleased to announce the *Galactic Blog
<https://galaxyproject.org/blog/>,* a place for blogging about Galaxy and
your experiences with it. The blog is on the Galaxy Hub
<https://galaxyproject.org/> and can be reached from the home page and the
Hub's Community menu.
Our very first post
about the ELIXIR Galaxy Community and was written by Frederik Coppens,
Gildas Le Corguillé, and Björn Grüning. We have a few more posts lined up
over the next week or so, but after that ...
*The Galactic Blog needs you! *If you've done something that others would
benefit from knowing about then please create a Galactic Blog post
describing your experiences. See the CONTRIBUTING
page. If you have questions, please let me know.
Blog posts can either be directly created in the Galactic Blog (and hosted
on the Galaxy Hub <https://galaxyproject.org/>), or can be posted on your
favorite blogging platform (see, for example, Galactic Engineer
<http://galacticengineer.blogspot.co.uk/>) and linked to from the Galactic
Blog. We'll tweet about every entry and highlight them in the monthly
newsletter as well.
Finally, this was a team effort and I'd particularly like to thank Dannon
Baker, Björn Grüning, and Martin Čech for their contributions.
I look forward to reading your blog posts!
PS: The Galactic Blog replaces the former *Community Log* and includes all
content from it (which is why, even though the blog is new, it includes
entries back to 2013).
I am trying to invoke a workflow on a paired dataset collection (simple trim step (trimmomatic) followed by align (RNAStar)) through the GUI.
Each time I run, I get the prompt:
Successfully invoked workflow RNASeq v1.0.
You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered
suggesting that all is well, but nothing gets added to my history. I am not sending data to another history, but to the current one.
If I look into the logs, I see the error AttributeError: 'object' object has no attribute 'collection' as the reason for failing
If I modify the workflow to work on individual datasets, it runs successfully. It seems to be purely when I run on collections.
This is my own Galaxy instance (17.05), not the public server.
Any help appreciated
Tony (Galaxy Newbie)
Could you please let me know if there a webDAV client in Galaxy.
I would to implment a tool using the webDav client to let Galaxy
communicate with another database to bring data from a database into
Hi dev team,
I have a very big problem since I updated to galaxy 17.05 with
deeptools from toolshed.
Due to a bug in galaxy 17.05 with toolshed installed tools (reported
in this issue https://github.com/galaxyproject/galaxy/issues/4591), I
re-installed deeptools to try to resolve it.
Not resolved really but it's another problem. I temporarly bypassed it.
Here is my problem : I've installed deeptools from toolshed and when
we try to use "compute matrix" for example, we have this error message
Fatal error: Exit code 1 ()
Traceback (most recent call last):
File "/usr/local/bin/computeMatrix", line 4, in <module>
from deeptools.computeMatrix import main
ImportError: No module named deeptools.computeMatrix
It seems that wrapper are installed but not the tool "deeptools".
For more information, here it's the way for the installation :
search and install via toolshed
Install "suite_deeptools" (version 184.108.40.206.0 : 3d68b716965a)
Info in Manage tool dependencies : version=2.5.1, resolver=Conda,
green check symbol in the line with a list of all deeptools.
Galaxy 17.05, commit cfabe37 (21 sept 2017)
I've tried to uninstall/reinstall dependencies with conda but without success.
Have you any idea to install the deeptools please ?
I'm stuck on trying to index genome references for gatk. From what i see it happens (no space left) when the script try to create dictionnary (even it being small..).
Anyway, using java, i tried the usual arguments, without success and now i don't know what to do/where to look anymore.
For other picard tools, i just overwrote some arguments through job_conf.xml so for a start i added this one to the destination.
After that, i've looked in the python script and tried to add to it the same arguments (previous attempt had been unsuccesful).
Any ideas about "how to define a directory other than /tmp" ? Our cluster is made with small tmp dirs on all its nodes.
The actual attempts are :
data_manager_gatk_picard_index_builder.py line 40 :
args = [ 'java', '-Xmx5120m', '-Djava.io.tmpdir=/local', '-jar', jar, 'R=%s' % gatk_sorted_fasta_filename, 'O=%s.dict' % sequence_id ]
<destination id="java_heavy" runner="drmaa">
<param id="nativeSpecification">-p kosmos --mem-per-cpu=5120 --ntasks-per-node=4 --nodes=1</param>
<env id="_JAVA_OPTIONS">-Xmx5120m -Djava.io.tmpdir=/local</env>
University of Liège, GIGA +1
+32 4 366 34 53
+32 497 87 96 46
I'm new to Galaxy and have been tasked with learning how to admin it.
We are running commit 407da92f88ac859d3f9b259be83640516159fe15
I notice there is a screen called "Manage Jobs".
How to I re-order, re-prioritise or pause jobs in that list?
It seems to only have the options to stop (which I presume cannot be
restarted because it's called stop not pause), and Job Lock, which I
presume controls if users can or cannot submit jobs, rather than locking
Are my assumptions incorrect - is one of these options a "pause" option?
"The antidote to apocalypticism is *apocalyptic civics*. Apocalyptic civics
is the insistence that we cannot ignore the truth, nor should we panic
about it. It is a shared consciousness that our institutions have failed
and our ecosystem is collapsing, yet we are still here — and we are
creative agents who can shape our destinies. Apocalyptic civics is the
conviction that the only way out is through, and the only way through is
*Greg Bloom* @greggish