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 [[email protected]] 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 <[email protected]>
*Sent:* 06 July 2018 10:15:12
*To:* Van Wageningen, GERHARD [[email protected]]
*Cc:* [email protected]
*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, [email protected] wrote:
Message: 1
Date: Thu, 5 Jul 2018 08:14:35 +0000
From: "Van Wageningen, GERHARD [[email protected]]"
<[email protected]>
To:"[email protected]"
<[email protected]>
Subject: [galaxy-dev] Conda problems: Failed to activate conda
environment
Message-ID:
<am0pr07mb4354eead1afb5809409f9f3692...@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,
[email protected], 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
-------------------------------------------
<http://www.sun.ac.za/english/Pages/Water-crisis.aspx>
The integrity and confidentiality of this email is governed by these
terms. Disclaimer <http://www.sun.ac.za/emaildisclaimer >
Die integriteit en vertroulikheid van hierdie e-pos word deur die
volgende bepalings gereël. Vrywaringsklousule
<http://www.sun.ac.za/emaildisclaimer >
--
-------------------------------------------
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,
[email protected], 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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