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