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
--
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
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/