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> 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 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.



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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