conda bash environment problem as real user

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conda bash environment problem as real user

Matthias Bernt
Dear list,

our galaxy runs jobs as real user and I get the following error for
multiple tools:

"""
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.

Cheers,
Matthias

P.S.: https://github.com/galaxyproject/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 482296,
[hidden email], www.ufz.de

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
-------------------------------------------
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Re: conda bash environment problem as real user

Gildas Le Corguillé
Hi,

workaround#2 : use the new admin interface "Manage Tool Dependencies" : https://galaxyproject.github.io/training-material/topics/dev/tutorials/conda/slides.html#18

It will allow you to create Conda environments and individual package with the user galaxy (and check if you miss some of them).

My 2 cents

Gildas

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Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org

Station Biologique de Roscoff - UPMC/CNRS - FR2424
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Le 11 oct. 2017 à 16:41, Matthias Bernt <[hidden email]> a écrit :

Dear list,

our galaxy runs jobs as real user and I get the following error for multiple tools:

"""
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.

Cheers,
Matthias

P.S.: https://github.com/galaxyproject/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 482296,
[hidden email], www.ufz.de

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
-------------------------------------------
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/