Hi, workaround#2 : use the new admin interface "Manage Tool Dependencies" : https://galaxyproject.github.io/training-material/topics/dev/tutorials/conda... <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 ----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateform ABiMS (Analyses and Bioinformatics for Marine Science) http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/> Member of the Workflow4Metabolomics project http://workflow4metabolomics.org <http://workflow4metabolomics.org/> Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 ------------------------------------------------------------------

Le 11 oct. 2017 à 16:41, Matthias Bernt <m.bernt@ufz.de> 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

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------------------------------------------- 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.bernt@ufz.de, www.ufz.de

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