galaxy-dev

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galaxy-dev@lists.galaxyproject.org

July 2018

15 participants
12 discussions

From Paste to uWSGI
by Jochen Bick 09 Jul '18

09 Jul '18

Hi all, we would like to update to 18.05 and thereby also update our Paste Server. https://docs.galaxyproject.org/en/latest/admin/scaling.html Is there any tutorial on how to update from Paste to uWSGI? Cheers Jochen -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 8092 Zurich, Switzerland Office: Eschikon 27 8315 Lindau, Switzerland Phone +41 52 354 92 06 jochen.bick(a)usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> www.ap.ethz.ch

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Re: [galaxy-dev] Conda problems: Failed to activate conda environment
by Matthias Bernt 06 Jul '18

06 Jul '18

Dear Gerhard, I don't know about the python error.. could you tell us the output of `locale` when logged in as the user running the Galaxy server? For the second problem, I remember that I also have a similar problem. For some reasons some symlinks in the conda environment are not created. you can check if in the respective environment's bin directory symlinks to the conda, activate and deactivate binaries/scripts exist. If not you can fix the missing links (I run the following after each tool installation) ``` for env in "{{ galaxy_server_dir }}"/database/dependencies/_conda/envs/*; do for link in conda activate deactivate; do \[ -h $env/bin/$link \] || ln -s "{{ galaxy_server_dir }}"/database/dependencies/_conda/bin/$link $env/bin/$link; done done ``` Hope this helps. Cheers, Matthias On 05.07.2018 18:00, galaxy-dev-request(a)lists.galaxyproject.org wrote: > Message: 1 > Date: Thu, 5 Jul 2018 08:14:35 +0000 > From: "Van Wageningen, GERHARD [gerhardv(a)sun.ac.za]" > <gerhardv(a)sun.ac.za> > To:"galaxy-dev(a)lists.galaxyproject.org" > <galaxy-dev(a)lists.galaxyproject.org> > Subject: [galaxy-dev] Conda problems: Failed to activate conda > environment > Message-ID: > <AM0PR07MB4354EEAD1AFB5809409F9F3692400(a)AM0PR07MB4354.eurprd07.prod.outlook.com> > > Content-Type: text/plain; charset="iso-8859-1" > > Hi All > > I have recently started learning the Galaxy setup starting with an upgrade. > Made some headway but I was wondering if someone could comment on a problem that has emerged. > The system is a Galaxy 18.05 installation (upgraded from 17.01) on an Altair PBS scheduler with drmaa setup (working) > > Conda problem: Failed to activate conda environment. > > Conda works during tool installation or reinstallation. > > Galaxy tools have been updated/reinstalled so they all look "green" in manage tools. > > In Manage Dependencies there are a number of "Dependency resolved but version not found" warnings, otherwise the deps look clean. > > When running tools in Galaxy errors occur, after the jobs have correctly deployed on the cluster. > > > The galaxy application raised errors like the two below. > > "Failed to activate conda environment! Error was: > Fatal Python error: Py_Initialize: Unable to get the locale encoding > File "/home/.galaxy/tooldeps/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/__init__.py", line 123 > raise C" > > > " > > Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks. > > > " > > > Galaxy started and stopped using supervisord with config below: -- ------------------------------------------- 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(a)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 -------------------------------------------

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