The python error occurs with the bowtie2 installation. Other tools give other errors ...
I think the soft links may have sorted out a lot of that.
...still checking.
Björn Grüning suggested that I look at the sequence of tool dep lookups.
So: dependency_resolvers_conf.xml looks like this (below)... and the galaxy.ini file
points to the tooldeps folder in the usual way. I renamed the
dependency_resolvers_conf.xml file to force the installation to use the defaults and
reinstalled the bowtie2 package. Conda kicked in and did some work.
Now it seems as though it is generating errors based on the contents of the dataset ... so
I am guessing that there is something was wrong or missing with the
dependency_resolvers_conf.xml that was there.
Still going through the other tools to test them.
Thanks for your help.
dependency_resolvers_conf.xml file on system
<dependency_resolvers>
<!-- the default configuration, first look for dependencies installed from the toolshed
-->
<tool_shed_packages />
<!-- then look for env.sh files in directories according to the "galaxy
packages" schema.
These resolvers can take a base_path attribute to specify where to look for
package definitions, but by default look in the directory specified by
tool_dependency_dir
in Galaxy's config/galaxy.ini -->
<galaxy_packages />
<galaxy_packages versionless="true" />
<conda />
<conda versionless="true" />
<!-- Example configuration of modules dependency resolver, uses Environment Modules
-->
<!--
<modules modulecmd="/opt/Modules/3.2.9/bin/modulecmd" />
<modules modulecmd="/opt/Modules/3.2.9/bin/modulecmd"
versionless="true" default_indicator="default" />
Attributes are:
* modulecmd - path to modulecmd
* versionless - default: false - whether to resolve tools using a version number or not
* find_by - directory or avail - use the DirectoryModuleChecker or AvailModuleChecker
* prefetch - default: true - in the AvailModuleChecker prefetch module info with
'module avail'
* default_indicator - default: '(default)' - what indicate to the
AvailModuleChecker that a module is the default version
-->
<!-- other resolvers
<tool_shed_tap />
<homebrew />
-->
</dependency_resolvers>
New error message from Bowtie2 after disabling local dedependency_resolvers_conf.xml file
Fatal error: Exit code 127 ()
Building a SMALL index
Reference file does not seem to be a FASTA file
Error: Encountered internal Bowtie 2 exception (#1)
Command:
/home/.galaxy/tooldeps/_conda/envs/mulled-v1-7576289d51ff5aefa21c8a2af901e1a61eb245f4e5fd66ae894d120dd35ff8f6/bin/bowtie2-build-s
--wrapper basic-0 --threads 8 /home/.galaxy/database/files/013/dataset_13148.dat genome
Deleting "genome.3.bt2" file written during aborted indexing attempt.
Deleting "genome.4.bt2" file written during aborted indexing attempt.
Deleting "genome.1.bt2" file written during aborted indexing attempt.
Deleting "genome.2.bt2" file written during aborted indexing attempt.
/home/.galaxy/database/jobs_directory/007/7436/tool_script.sh: line 41: samtools: command
not found
(ERR): "genome" does not exist or is not a Bowtie 2 index
Exiting now ...
________________________________
From: Matthias Bernt <m.bernt(a)ufz.de>
Sent: 06 July 2018 10:42:12
To: Van Wageningen, GERHARD [gerhardv(a)sun.ac.za]
Cc: galaxy-dev(a)lists.galaxyproject.org
Subject: Re: Conda problems: Failed to activate conda environment
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(a)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(a)ufz.de>
*Sent:* 06 July 2018 10:15:12
*To:* Van Wageningen, GERHARD [gerhardv(a)sun.ac.za]
*Cc:* galaxy-dev(a)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(a)lists.galaxyproject.org wrote:
> Message: 1
> Date: Thu, 5 Jul 2018 08:14:35 +0000
> From: "Van Wageningen, GERHARD [gerhardv(a)sun.ac.za]"
> <gerhardv(a)sun.ac.za>
> To:"galaxy-dev@lists.galaxyproject.org"
> <galaxy-dev(a)lists.galaxyproject.org>
> Subject: [galaxy-dev] Conda problems: Failed to activate conda
> environment
> Message-ID:
>
<AM0PR07MB4354EEAD1AFB5809409F9F3692400(a)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(a)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(a)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 terms.
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