Hi Gerhard,

wonderful.

For the other problem: you seem to use a tool that still uses a toolshed
package (python in this case) instead of the conda dependency. Can you
make sure that you ensure that conda is used for dependency resolution?

Otherwise, which tool are you trying to install?

Cheers,
Matthias

On 06.07.2018 10:38, Van Wageningen, GERHARD [gerhardv@sun.ac.za] wrote:
> Hi Matthias - thanx for the missing link tip - that fixes that ...
>
>
> Locale as Galaxy user is
>
>
> [galaxy@storage1 ~]$ locale
> LANG=en_US.UTF-8
> LC_CTYPE="en_US.UTF-8"
> LC_NUMERIC="en_US.UTF-8"
> LC_TIME="en_US.UTF-8"
> LC_COLLATE="en_US.UTF-8"
> LC_MONETARY="en_US.UTF-8"
> LC_MESSAGES="en_US.UTF-8"
> LC_PAPER="en_US.UTF-8"
> LC_NAME="en_US.UTF-8"
> LC_ADDRESS="en_US.UTF-8"
> LC_TELEPHONE="en_US.UTF-8"
> LC_MEASUREMENT="en_US.UTF-8"
> LC_IDENTIFICATION="en_US.UTF-8"
> LC_ALL=
>
>
> ------------------------------------------------------------------------
> *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;
>         done
>       done
> ```
>
> Hope this helps.
>
> Cheers,
> Matthias
>
> 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
>
> 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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>
> The integrity and confidentiality of this email is governed by these
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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
-------------------------------------------