Dear Enis, thanks for the answer. I was not suggesting anything -- just asking. I just found the answer myself (https://virtualenv.pypa.io/en/stable/) "a virtualenv uses the system Python’s standard library but contains its own copy of the Python interpreter". Best, Matthias On 01.03.2017 15:27, Enis Afgan wrote:
Hi Matthias, I'm not sure I understand what you're suggesting here, if anything? Granted, I haven't used software collections but this problem feels like it has more to do with it, where the libpython is not installed as part of the Python install there. Perhaps a manual install of the library with the software collection enabled would fix this (http://stackoverflow.com/questions/26597527/how-to-install-libpython2-7-so). The library cannot just be included into requirements.txt for example.
On Mon, Feb 27, 2017 at 2:27 AM, Matthias Bernt <m.bernt@ufz.de <mailto:m.bernt@ufz.de>> wrote:
Dear galaxy developers,
Is it expected that the virtualenv in .venv/ does include the python binary but does not include the python shared libraries?
Some more details:
I have installed galaxy on CentOS 6.8 which includes the required python 2.7 only via software collections. For the installation of galaxy I have enabled the software collection by calling "source /opt/rh/python27/enable" (which sets PATH, LD_LIBRARY_PATH, MANPATH, XDG_DATA_DIRS, and PKG_CONFIG_PATH).
Currently I was trying to run the ansible role ansible-galaxy-tools from https://github.com/galaxyproject/ansible-galaxy-tools <https://github.com/galaxyproject/ansible-galaxy-tools> which runs "/home/galaxy/galaxy/.venv/bin/python manage_bootstrap_user.py ..." and gives me /home/galaxy/galaxy/.venv/bin/python: error while loading shared libraries: libpython2.7.so.1.0: cannot open shared object file: No such file or directory.
This python call would work if I again "source /opt/rh/python27/enable". But then the venv python binary is used with the library of the system. Intuitively I would expect that the library and binary belong together.
Cheers, Matthias
--
------------------------------------------- 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 <tel:%2B49%20341%20235%20482296>, m.bernt@ufz.de <mailto:m.bernt@ufz.de>, www.ufz.de <http://www.ufz.de>
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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 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 -------------------------------------------