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ansible-galaxy-tools and venv

Matthias Bernt
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.

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,
[hidden email], 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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Re: ansible-galaxy-tools and venv

Enis Afgan
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 <[hidden email]> 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.

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 <a href="tel:%2B49%20341%20235%20482296" value="+49341235482296" target="_blank">+49 341 235 482296,
[hidden email], 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/mailinglists/


___________________________________________________________
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:
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Re: ansible-galaxy-tools and venv

Matthias Bernt
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 <[hidden email]
> <mailto:[hidden email]>> 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>,
>     [hidden email] <mailto:[hidden email]>, www.ufz.de <http://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/ <https://lists.galaxyproject.org/>
>
>     To search Galaxy mailing lists use the unified search at:
>       http://galaxyproject.org/search/mailinglists/
>     <http://galaxyproject.org/search/mailinglists/>
>
>
--

-------------------------------------------
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,
[hidden email], 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/mailinglists/

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