Hi Matthias - thanx for the missing link tip - that fixes that ...

Locale as Galaxy user is

[galaxy@storage1 ~]$ locale

From: Matthias Bernt <m.bernt@ufz.de>
Sent: 06 July 2018 10:15:12
To: Van Wageningen, GERHARD [gerhardv@sun.ac.za]
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: Conda problems: Failed to activate conda environment
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;

Hope this helps.


On 05.07.2018 18:00, galaxy-dev-request@lists.galaxyproject.org wrote:
> Message: 1
> Date: Thu, 5 Jul 2018 08:14:35 +0000
> From: "Van Wageningen, GERHARD [gerhardv@sun.ac.za]"
>        <gerhardv@sun.ac.za>
> To:"galaxy-dev@lists.galaxyproject.org"
>        <galaxy-dev@lists.galaxyproject.org>
> Subject: [galaxy-dev] Conda problems: Failed to activate conda
>        environment
> Message-ID:
>        <AM0PR07MB4354EEAD1AFB5809409F9F3692400@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@ufz.de, www.ufz.de

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