Conda problems: Failed to activate conda environment

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Conda problems: Failed to activate conda environment

Van Wageningen, GERHARD [gerhardv@sun.ac.za]

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:


Thanks, hopefully someone has seen this before ...


regards, Gerhard



[program:web]
command         = uwsgi --plugin python --virtualenv /home/.galaxy/.venv --ini-paste /home/.galaxy/config/galaxy.ini
directory       = /home/.galaxy
umask           = 022
autostart       = true
autorestart     = true
startsecs       = 10
user            = galaxy
numprocs        = 1
stopsignal      = INT

[program:handler]
command         = python ./scripts/galaxy-main -c /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s
directory       = /home/.galaxy
process_name    = handler%(process_num)s
numprocs        = 1
umask           = 022
autostart       = true
autorestart     = true
startsecs       = 10
user            = galaxy
environment     = VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/"
stdout_logfile  = /home/.galaxy/handler%(process_num)s.log
redirect_stderr = true

[group:galaxy]
programs        = handler, web


The integrity and confidentiality of this email is governed by these terms. Disclaimer
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule

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Re: Conda problems: Failed to activate conda environment

Björn Grüning-3
Hi Gerhard,

it seems your tool is picking up the old tool_dependency version and not
the conda version of python.

Have a look at
https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample 
to configure the order of dependency resolution in Galaxy.

Cheers,
Bjoern

> 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:
>
>
> Thanks, hopefully someone has seen this before ...
>
>
> regards, Gerhard
>
>
>
> [program:web]
> command         = uwsgi --plugin python --virtualenv /home/.galaxy/.venv
> --ini-paste /home/.galaxy/config/galaxy.ini
> directory       = /home/.galaxy
> umask           = 022
> autostart       = true
> autorestart     = true
> startsecs       = 10
> user            = galaxy
> numprocs        = 1
> stopsignal      = INT
>
> [program:handler]
> command         = python ./scripts/galaxy-main -c
> /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s
> directory       = /home/.galaxy
> process_name    = handler%(process_num)s
> numprocs        = 1
> umask           = 022
> autostart       = true
> autorestart     = true
> startsecs       = 10
> user            = galaxy
> environment     =
> VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/"
> stdout_logfile  = /home/.galaxy/handler%(process_num)s.log
> redirect_stderr = true
>
> [group:galaxy]
> programs        = handler, web
>
> <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 >
>
>
> ___________________________________________________________
> 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/
>
___________________________________________________________
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/

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Re: Conda problems: Failed to activate conda environment

Matthias Bernt
In reply to this post by Van Wageningen, GERHARD [gerhardv@sun.ac.za]
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, [hidden email] wrote:

> Message: 1
> Date: Thu, 5 Jul 2018 08:14:35 +0000
> From: "Van Wageningen, GERHARD [[hidden email]]"
> <[hidden email]>
> To:"[hidden email]"
> <[hidden email]>
> Subject: [galaxy-dev] Conda problems: Failed to activate conda
> environment
> Message-ID:
> <[hidden email]>
>
> 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,
[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:
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Re: Conda problems: Failed to activate conda environment

Van Wageningen, GERHARD [gerhardv@sun.ac.za]

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 <[hidden email]>
Sent: 06 July 2018 10:15:12
To: Van Wageningen, GERHARD [[hidden email]]
Cc: [hidden email]
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, [hidden email] wrote:
> Message: 1
> Date: Thu, 5 Jul 2018 08:14:35 +0000
> From: "Van Wageningen, GERHARD [[hidden email]]"
>        <[hidden email]>
> To:"[hidden email]"
>        <[hidden email]>
> Subject: [galaxy-dev] Conda problems: Failed to activate conda
>        environment
> Message-ID:
>        <[hidden email]>
>       
> 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,
[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
-------------------------------------------

The integrity and confidentiality of this email is governed by these terms. Disclaimer
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule

___________________________________________________________
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/
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Re: Conda problems: Failed to activate conda environment

Matthias Bernt
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 [[hidden email]] 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 <[hidden email]>
> *Sent:* 06 July 2018 10:15:12
> *To:* Van Wageningen, GERHARD [[hidden email]]
> *Cc:* [hidden email]
> *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, [hidden email] wrote:
>> Message: 1
>> Date: Thu, 5 Jul 2018 08:14:35 +0000
>> From: "Van Wageningen, GERHARD [[hidden email]]"
>>        <[hidden email]>
>> To:"[hidden email]"
>>        <[hidden email]>
>> Subject: [galaxy-dev] Conda problems: Failed to activate conda
>>        environment
>> Message-ID:
>>        <[hidden email]>
>>        
>> 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,
> [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
> -------------------------------------------
> <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,
[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/
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Re: Conda problems: Failed to activate conda environment

Van Wageningen, GERHARD [gerhardv@sun.ac.za]

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 <[hidden email]>
Sent: 06 July 2018 10:42:12
To: Van Wageningen, GERHARD [[hidden email]]
Cc: [hidden email]
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 [[hidden email]] 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 <[hidden email]>
> *Sent:* 06 July 2018 10:15:12
> *To:* Van Wageningen, GERHARD [[hidden email]]
> *Cc:* [hidden email]
> *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, [hidden email] wrote:
>> Message: 1
>> Date: Thu, 5 Jul 2018 08:14:35 +0000
>> From: "Van Wageningen, GERHARD [[hidden email]]"
>>        <[hidden email]>
>> To:"[hidden email]"
>>        <[hidden email]>
>> Subject: [galaxy-dev] Conda problems: Failed to activate conda
>>        environment
>> Message-ID:
>>        <[hidden email]>
>>       
>> 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,
> [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
> -------------------------------------------
> <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,
[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
-------------------------------------------

The integrity and confidentiality of this email is governed by these terms. Disclaimer
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule

___________________________________________________________
Please keep all replies on the list by using "reply all"
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Re: Conda problems: Failed to activate conda environment

Van Wageningen, GERHARD [gerhardv@sun.ac.za]
In reply to this post by Björn Grüning-3

Hi Bjoern, thanks for the pointer ... We are running the default dependency_resolvers_conf.xml now and that, along with the symlinks hint has helped with a lot of the tool dep. issues.  But there is still a pathing issue we are stuck on.

Take for example the trim_galore tool.

The error is 

/home/.galaxy/database/jobs_directory/007/7480/tool_script.sh: line 25: trim_galore: command not found

And the script is:

#!/bin/bash

# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
    exit 42
fi
[ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
    . /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3' > conda_activate.log 2>&1
    if [ $? -eq 0 ];then
        break
    else
        let COUNT=COUNT+1
        if [ $COUNT -eq $MAX_TRIES ];then
            echo "Failed to activate conda environment! Error was:"
            cat conda_activate.log
            exit 1
        fi
        sleep 10s
    fi
done ; trim_galore --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7477 2>&1; ln -s '/home/.galaxy/database/files/013/dataset_13139.dat' input_1.fastq &&  trim_galore  --phred33    --output_dir ./      input_1.fastq  --dont_gzip  && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi



In fact most of the tools do this post-upgrade - where they cannot find a file.

Here is the trace from hisat2 - it fails in a similar way so we conclude that there is a common underlying fault here that is affecting the pathing of the scripts.

Any ideas how we should go about finding this error?

Thanks, Gerhard

PS Here is the hisat2 output.

#!/bin/bash

 

# The following block can be used by the job system

# to ensure this script is runnable before actually attempting

# to run it.

if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then

    exit 42

fi

[ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] ||

MAX_TRIES=3

COUNT=0

while [ $COUNT -lt $MAX_TRIES ]; do

    . /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426' > conda_activate.log 2>&1

    if [ $? -eq 0 ];then

        break

    else

        let COUNT=COUNT+1

        if [ $COUNT -eq $MAX_TRIES ];then

            echo "Failed to activate conda environment! Error was:"

            cat conda_activate.log

            exit 1

        fi

        sleep 10s

    fi

done ; [ "$CONDA_DEFAULT_ENV" = "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426" ] ||

MAX_TRIES=3

COUNT=0

while [ $COUNT -lt $MAX_TRIES ]; do

    . /home/.galaxy/tooldeps/_conda/bin/activate '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426' > conda_activate.log 2>&1

    if [ $? -eq 0 ];then

        break

    else

        let COUNT=COUNT+1

        if [ $COUNT -eq $MAX_TRIES ];then

            echo "Failed to activate conda environment! Error was:"

            cat conda_activate.log

            exit 1

        fi

        sleep 10s

    fi

done ; hisat2 --version > /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7484 2>&1; set -o | grep -q pipefail && set -o pipefail;   ln -s '/home/.galaxy/database/files/013/dataset_13248.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome &&        ln -f -s '/home/.galaxy/database/files/013/dataset_13238.dat' input_f.fastq &&  ln -f -s '/home/.galaxy/database/files/013/dataset_13243.dat' input_r.fastq &&     hisat2  -p ${GALAXY_SLOTS:-1}  -x 'genome'     -1 'input_f.fastq' -2 'input_r.fastq'                               | samtools sort - -@ ${GALAXY_SLOTS:-1} -l 6 -o '/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat'

 

The job fails when it cannot find “hisat2-build”. 

 

Fatal error: Exit code 127 ()

/home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41: hisat2-build: command not found

 

The PATH variable should be exported with installation (/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh):

 

PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH; export PATH

HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT2_ROOT_DIR

HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; export HISAT_ROOT_DIR

 

The conda environment with dependencies seems to be there:

 

/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin




Björn Grüning <[hidden email]>;


From: Björn Grüning <[hidden email]>
Sent: 05 July 2018 22:00:58
To: Van Wageningen, GERHARD [[hidden email]]; [hidden email]
Subject: Re: [galaxy-dev] Conda problems: Failed to activate conda environment
 
Hi Gerhard,

it seems your tool is picking up the old tool_dependency version and not
the conda version of python.

Have a look at
https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample


to configure the order of dependency resolution in Galaxy.

Cheers,
Bjoern

> 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:
>
>
> Thanks, hopefully someone has seen this before ...
>
>
> regards, Gerhard
>
>
>
> [program:web]
> command         = uwsgi --plugin python --virtualenv /home/.galaxy/.venv
> --ini-paste /home/.galaxy/config/galaxy.ini
> directory       = /home/.galaxy
> umask           = 022
> autostart       = true
> autorestart     = true
> startsecs       = 10
> user            = galaxy
> numprocs        = 1
> stopsignal      = INT
>
> [program:handler]
> command         = python ./scripts/galaxy-main -c
> /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s
> directory       = /home/.galaxy
> process_name    = handler%(process_num)s
> numprocs        = 1
> umask           = 022
> autostart       = true
> autorestart     = true
> startsecs       = 10
> user            = galaxy
> environment     =
> VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/"
> stdout_logfile  = /home/.galaxy/handler%(process_num)s.log
> redirect_stderr = true
>
> [group:galaxy]
> programs        = handler, web
>
> <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 >
>
>
> ___________________________________________________________
> 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/
>

The integrity and confidentiality of this email is governed by these terms. Disclaimer
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule

___________________________________________________________
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/

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  http://galaxyproject.org/search/
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Open this post in threaded view
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Re: Conda problems: Failed to activate conda environment

Björn Grüning-3
Hi,

can you do:

  . /home/.galaxy/tooldeps/_conda/bin/activate
'/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3

And see if you can execute trim_galore from the commandline and get the
help?

Ciao,
Bjoern

Am 10.07.2018 um 08:34 schrieb Van Wageningen, GERHARD [[hidden email]]:

> Hi Bjoern, thanks for the pointer ... We are running the default
> dependency_resolvers_conf.xml now and that, along with the symlinks hint
> has helped with a lot of the tool dep. issues.  But there is still a
> pathing issue we are stuck on.
>
> Take for example the trim_galore tool.
>
> The error is
>
> /home/.galaxy/database/jobs_directory/007/7480/tool_script.sh: line 25:
> trim_galore: command not found
>
> And the script is:
>
> #!/bin/bash
>
> # The following block can be used by the job system
> # to ensure this script is runnable before actually attempting
> # to run it.
> if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
>      exit 42
> fi
> [ "$CONDA_DEFAULT_ENV" =
> "/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3" ] ||
> MAX_TRIES=3
> COUNT=0
> while [ $COUNT -lt $MAX_TRIES ]; do
>      . /home/.galaxy/tooldeps/_conda/bin/activate
> '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3' >
> conda_activate.log 2>&1
>      if [ $? -eq 0 ];then
>          break
>      else
>          let COUNT=COUNT+1
>          if [ $COUNT -eq $MAX_TRIES ];then
>              echo "Failed to activate conda environment! Error was:"
>              cat conda_activate.log
>              exit 1
>          fi
>          sleep 10s
>      fi
> done ; trim_galore --version >
> /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7477 2>&1; ln -s
> '/home/.galaxy/database/files/013/dataset_13139.dat' input_1.fastq &&  
> trim_galore  --phred33    --output_dir ./      input_1.fastq  
> --dont_gzip  && if [ -f input_1_trimmed.fq.gz ] ; then mv
> input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f
> input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ;
> fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz
> input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv
> input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f
> input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz
> input_2_unpaired_2.fq ; fi
>
>
>
> In fact most of the tools do this post-upgrade - where they cannot find
> a file.
>
> Here is the trace from hisat2 - it fails in a similar way so we conclude
> that there is a common underlying fault here that is affecting the
> pathing of the scripts.
>
> Any ideas how we should go about finding this error?
>
> Thanks, Gerhard
>
> PS Here is the hisat2 output.
>
> #!/bin/bash
>
> # The following block can be used by the job system
>
> # to ensure this script is runnable before actually attempting
>
> # to run it.
>
> if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
>
>      exit 42
>
> fi
>
> [ "$CONDA_DEFAULT_ENV" =
> "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426"
> ] ||
>
> MAX_TRIES=3
>
> COUNT=0
>
> while [ $COUNT -lt $MAX_TRIES ]; do
>
>      . /home/.galaxy/tooldeps/_conda/bin/activate
> '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
>  > conda_activate.log 2>&1
>
>      if [ $? -eq 0 ];then
>
>          break
>
>      else
>
>          let COUNT=COUNT+1
>
>          if [ $COUNT -eq $MAX_TRIES ];then
>
>              echo "Failed to activate conda environment! Error was:"
>
>              cat conda_activate.log
>
>              exit 1
>
>          fi
>
>          sleep 10s
>
>      fi
>
> done ; [ "$CONDA_DEFAULT_ENV" =
> "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426"
> ] ||
>
> MAX_TRIES=3
>
> COUNT=0
>
> while [ $COUNT -lt $MAX_TRIES ]; do
>
>      . /home/.galaxy/tooldeps/_conda/bin/activate
> '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
>  > conda_activate.log 2>&1
>
>      if [ $? -eq 0 ];then
>
>          break
>
>      else
>
>          let COUNT=COUNT+1
>
>          if [ $COUNT -eq $MAX_TRIES ];then
>
>              echo "Failed to activate conda environment! Error was:"
>
>              cat conda_activate.log
>
>              exit 1
>
>          fi
>
>          sleep 10s
>
>      fi
>
> done ; hisat2 --version >
> /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7484 2>&1; set -o | grep -q
> pipefail && set -o pipefail;   ln -s
> '/home/.galaxy/database/files/013/dataset_13248.dat' genome.fa &&
> _hisat2-build_ -p ${GALAXY_SLOTS:-1} genome.fa genome &&        ln -f -s
> '/home/.galaxy/database/files/013/dataset_13238.dat' input_f.fastq &&  
> ln -f -s '/home/.galaxy/database/files/013/dataset_13243.dat'
> input_r.fastq &&     hisat2  -p ${GALAXY_SLOTS:-1}  -x 'genome'     -1
> 'input_f.fastq' -2 'input_r.fastq'                               |
> samtools sort - -@ ${GALAXY_SLOTS:-1} -l 6 -o
> '/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat'
>
> The job fails when it cannot find “hisat2-build”.
>
> Fatal error: Exit code 127 ()
>
> /home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41:
> hisat2-build: command not found
>
> The PATH variable should be exported with installation
> (/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh):
>
> PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH;
> export PATH
>
> HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43;
> export HISAT2_ROOT_DIR
>
> HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43;
> export HISAT_ROOT_DIR
>
> The conda environment with dependencies seems to be there:
>
> /home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin
>
>
>
>
> Björn Grüning <[hidden email]>;
> [hidden email]
>
> ------------------------------------------------------------------------
> *From:* Björn Grüning <[hidden email]>
> *Sent:* 05 July 2018 22:00:58
> *To:* Van Wageningen, GERHARD [[hidden email]];
> [hidden email]
> *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
> environment
> Hi Gerhard,
>
> it seems your tool is picking up the old tool_dependency version and not
> the conda version of python.
>
> Have a look at
> https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample 
>
> <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
>
> galaxyproject/galaxy
> <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
> github.com
> galaxy - Data intensive science for everyone.
>
>
>
> to configure the order of dependency resolution in Galaxy.
>
> Cheers,
> Bjoern
>
>> 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:
>>
>>
>> Thanks, hopefully someone has seen this before ...
>>
>>
>> regards, Gerhard
>>
>>
>>
>> [program:web]
>> command         = uwsgi --plugin python --virtualenv /home/.galaxy/.venv
>> --ini-paste /home/.galaxy/config/galaxy.ini
>> directory       = /home/.galaxy
>> umask           = 022
>> autostart       = true
>> autorestart     = true
>> startsecs       = 10
>> user            = galaxy
>> numprocs        = 1
>> stopsignal      = INT
>>
>> [program:handler]
>> command         = python ./scripts/galaxy-main -c
>> /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s
>> directory       = /home/.galaxy
>> process_name    = handler%(process_num)s
>> numprocs        = 1
>> umask           = 022
>> autostart       = true
>> autorestart     = true
>> startsecs       = 10
>> user            = galaxy
>> environment     =
>> VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/"
>> stdout_logfile  = /home/.galaxy/handler%(process_num)s.log
>> redirect_stderr = true
>>
>> [group:galaxy]
>> programs        = handler, web
>>
>> <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 >
>>
>>
>> ___________________________________________________________
>> 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/
>>
> <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 >
___________________________________________________________
Please keep all replies on the list by using "reply all"
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Re: Conda problems: Failed to activate conda environment

Van Wageningen, GERHARD [gerhardv@sun.ac.za]

Hi - tx for (fast) reply.  Ok ... with this result ...


(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ trim_galore --version
-bash: trim_galore: command not found

Environment is:

(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ env
XDG_SESSION_ID=45352
HOSTNAME=storage1.hpc
SELINUX_ROLE_REQUESTED=
TERM=xterm-256color
SHELL=/bin/bash
HISTSIZE=1000
SSH_CLIENT=10.55.40.3 55438 22
PERL5LIB=/root/perl5/lib/perl5:/usr/local/lib/perl5:
SELINUX_USE_CURRENT_RANGE=
QTDIR=/usr/lib64/qt-3.3
OLDPWD=/home/.galaxy/tooldeps/_conda/envs/__hisat2@2.1.0
QTINC=/usr/lib64/qt-3.3/include
PERL_MB_OPT=--install_base /root/perl5
SSH_TTY=/dev/pts/2
QT_GRAPHICSSYSTEM_CHECKED=1
USER=root
LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
MAIL=/var/spool/mail/root
PATH=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3/bin:/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
CONDA_PREFIX=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
CONDA=/home/.galaxy/tooldeps/_conda
PWD=/home/.galaxy/tooldeps/_conda/envs
LANG=en_ZA.UTF-8
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/apps/etc/modulefiles
LOADEDMODULES=
KDEDIRS=/usr
PS1=(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) \[\e[1;31;40m\][\u@\h \w]$\[\e[0m\] 
SELINUX_LEVEL_REQUESTED=
HISTCONTROL=ignoredups
SHLVL=1
HOME=/root
CONDA_PS1_BACKUP=\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\] 
PERL_LOCAL_LIB_ROOT=:/root/perl5
LOGNAME=root
QTLIB=/usr/lib64/qt-3.3/lib
SSH_CONNECTION=10.55.40.3 55438 10.55.40.1 22
MODULESHOME=/usr/share/Modules
CONDA_DEFAULT_ENV=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
LESSOPEN=||/usr/bin/lesspipe.sh %s
XDG_RUNTIME_DIR=/run/user/0
QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
PERL_MM_OPT=INSTALL_BASE=/root/perl5
XAUTHORITY=/tmp/.Xauthority.root
BASH_FUNC_module()=() {  eval `/usr/bin/modulecmd bash $*`
}
_=/usr/bin/env
(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 /home/.galaxy/tooldeps/_conda/envs]$ 



From: Björn Grüning <[hidden email]>
Sent: 10 July 2018 08:38:15
To: Van Wageningen, GERHARD [[hidden email]]; [hidden email]
Subject: Re: [galaxy-dev] Conda problems: Failed to activate conda environment
 
Hi,

can you do:

  . /home/.galaxy/tooldeps/_conda/bin/activate
'/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3

And see if you can execute trim_galore from the commandline and get the
help?

Ciao,
Bjoern

Am 10.07.2018 um 08:34 schrieb Van Wageningen, GERHARD [[hidden email]]:
> Hi Bjoern, thanks for the pointer ... We are running the default
> dependency_resolvers_conf.xml now and that, along with the symlinks hint
> has helped with a lot of the tool dep. issues.  But there is still a
> pathing issue we are stuck on.
>
> Take for example the trim_galore tool.
>
> The error is
>
> /home/.galaxy/database/jobs_directory/007/7480/tool_script.sh: line 25:
> trim_galore: command not found
>
> And the script is:
>
> #!/bin/bash
>
> # The following block can be used by the job system
> # to ensure this script is runnable before actually attempting
> # to run it.
> if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
>      exit 42
> fi
> [ "$CONDA_DEFAULT_ENV" =
> "/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3" ] ||
> MAX_TRIES=3
> COUNT=0
> while [ $COUNT -lt $MAX_TRIES ]; do
>      . /home/.galaxy/tooldeps/_conda/bin/activate
> '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3' >
> conda_activate.log 2>&1
>      if [ $? -eq 0 ];then
>          break
>      else
>          let COUNT=COUNT+1
>          if [ $COUNT -eq $MAX_TRIES ];then
>              echo "Failed to activate conda environment! Error was:"
>              cat conda_activate.log
>              exit 1
>          fi
>          sleep 10s
>      fi
> done ; trim_galore --version >
> /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7477 2>&1; ln -s
> '/home/.galaxy/database/files/013/dataset_13139.dat' input_1.fastq && 
> trim_galore  --phred33    --output_dir ./      input_1.fastq 
> --dont_gzip  && if [ -f input_1_trimmed.fq.gz ] ; then mv
> input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f
> input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ;
> fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz
> input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv
> input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f
> input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz
> input_2_unpaired_2.fq ; fi
>
>
>
> In fact most of the tools do this post-upgrade - where they cannot find
> a file.
>
> Here is the trace from hisat2 - it fails in a similar way so we conclude
> that there is a common underlying fault here that is affecting the
> pathing of the scripts.
>
> Any ideas how we should go about finding this error?
>
> Thanks, Gerhard
>
> PS Here is the hisat2 output.
>
> #!/bin/bash
>
> # The following block can be used by the job system
>
> # to ensure this script is runnable before actually attempting
>
> # to run it.
>
> if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
>
>      exit 42
>
> fi
>
> [ "$CONDA_DEFAULT_ENV" =
> "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426"
> ] ||
>
> MAX_TRIES=3
>
> COUNT=0
>
> while [ $COUNT -lt $MAX_TRIES ]; do
>
>      . /home/.galaxy/tooldeps/_conda/bin/activate
> '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
>  > conda_activate.log 2>&1
>
>      if [ $? -eq 0 ];then
>
>          break
>
>      else
>
>          let COUNT=COUNT+1
>
>          if [ $COUNT -eq $MAX_TRIES ];then
>
>              echo "Failed to activate conda environment! Error was:"
>
>              cat conda_activate.log
>
>              exit 1
>
>          fi
>
>          sleep 10s
>
>      fi
>
> done ; [ "$CONDA_DEFAULT_ENV" =
> "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426"
> ] ||
>
> MAX_TRIES=3
>
> COUNT=0
>
> while [ $COUNT -lt $MAX_TRIES ]; do
>
>      . /home/.galaxy/tooldeps/_conda/bin/activate
> '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
>  > conda_activate.log 2>&1
>
>      if [ $? -eq 0 ];then
>
>          break
>
>      else
>
>          let COUNT=COUNT+1
>
>          if [ $COUNT -eq $MAX_TRIES ];then
>
>              echo "Failed to activate conda environment! Error was:"
>
>              cat conda_activate.log
>
>              exit 1
>
>          fi
>
>          sleep 10s
>
>      fi
>
> done ; hisat2 --version >
> /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7484 2>&1; set -o | grep -q
> pipefail && set -o pipefail;   ln -s
> '/home/.galaxy/database/files/013/dataset_13248.dat' genome.fa &&
> _hisat2-build_ -p ${GALAXY_SLOTS:-1} genome.fa genome &&        ln -f -s
> '/home/.galaxy/database/files/013/dataset_13238.dat' input_f.fastq && 
> ln -f -s '/home/.galaxy/database/files/013/dataset_13243.dat'
> input_r.fastq &&     hisat2  -p ${GALAXY_SLOTS:-1}  -x 'genome'     -1
> 'input_f.fastq' -2 'input_r.fastq'                               |
> samtools sort - -@ ${GALAXY_SLOTS:-1} -l 6 -o
> '/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat'
>
> The job fails when it cannot find “hisat2-build”.
>
> Fatal error: Exit code 127 ()
>
> /home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41:
> hisat2-build: command not found
>
> The PATH variable should be exported with installation
> (/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh):
>
> PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH;
> export PATH
>
> HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43;
> export HISAT2_ROOT_DIR
>
> HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43;
> export HISAT_ROOT_DIR
>
> The conda environment with dependencies seems to be there:
>
> /home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin
>
>
>
>
> Björn Grüning <[hidden email]>;
> [hidden email]
>
> ------------------------------------------------------------------------
> *From:* Björn Grüning <[hidden email]>
> *Sent:* 05 July 2018 22:00:58
> *To:* Van Wageningen, GERHARD [[hidden email]];
> [hidden email]
> *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
> environment
> Hi Gerhard,
>
> it seems your tool is picking up the old tool_dependency version and not
> the conda version of python.
>
> Have a look at
> https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample
>
> <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
>       
> galaxyproject/galaxy
> <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
> github.com
> galaxy - Data intensive science for everyone.
>
>
>
> to configure the order of dependency resolution in Galaxy.
>
> Cheers,
> Bjoern
>
>> 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:
>>
>>
>> Thanks, hopefully someone has seen this before ...
>>
>>
>> regards, Gerhard
>>
>>
>>
>> [program:web]
>> command         = uwsgi --plugin python --virtualenv /home/.galaxy/.venv
>> --ini-paste /home/.galaxy/config/galaxy.ini
>> directory       = /home/.galaxy
>> umask           = 022
>> autostart       = true
>> autorestart     = true
>> startsecs       = 10
>> user            = galaxy
>> numprocs        = 1
>> stopsignal      = INT
>>
>> [program:handler]
>> command         = python ./scripts/galaxy-main -c
>> /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s
>> directory       = /home/.galaxy
>> process_name    = handler%(process_num)s
>> numprocs        = 1
>> umask           = 022
>> autostart       = true
>> autorestart     = true
>> startsecs       = 10
>> user            = galaxy
>> environment     =
>> VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/"
>> stdout_logfile  = /home/.galaxy/handler%(process_num)s.log
>> redirect_stderr = true
>>
>> [group:galaxy]
>> programs        = handler, web
>>
>> <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 >
>>
>>
>> ___________________________________________________________
>> 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/
>>
> <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 >

The integrity and confidentiality of this email is governed by these terms. Disclaimer
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Re: Conda problems: Failed to activate conda environment

Björn Grüning-3
Which means that your conda envs are not what they are supposed to be.

You can fix this by removing the folder and let Galaxy re-created them,
but you should figure out why they are "empty". Maybe a wrong channel
priority or network issues during installation?

Hope that helps.
You could also from insite the env, do a `conda install ...`

> Hi - tx for (fast) reply.  Ok ... with this result ...
>
>
> (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
> /home/.galaxy/tooldeps/_conda/envs]$ trim_galore --version
> -bash: trim_galore: command not found
>
> Environment is:
>
> (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
> /home/.galaxy/tooldeps/_conda/envs]$ env
> XDG_SESSION_ID=45352
> HOSTNAME=storage1.hpc
> SELINUX_ROLE_REQUESTED=
> TERM=xterm-256color
> SHELL=/bin/bash
> HISTSIZE=1000
> SSH_CLIENT=10.55.40.3 55438 22
> PERL5LIB=/root/perl5/lib/perl5:/usr/local/lib/perl5:
> SELINUX_USE_CURRENT_RANGE=
> QTDIR=/usr/lib64/qt-3.3
> OLDPWD=/home/.galaxy/tooldeps/_conda/envs/__hisat2@2.1.0
> QTINC=/usr/lib64/qt-3.3/include
> PERL_MB_OPT=--install_base /root/perl5
> SSH_TTY=/dev/pts/2
> QT_GRAPHICSSYSTEM_CHECKED=1
> USER=root
> LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
> MAIL=/var/spool/mail/root
> PATH=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3/bin:/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
> CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
> CONDA_PREFIX=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
> CONDA=/home/.galaxy/tooldeps/_conda
> PWD=/home/.galaxy/tooldeps/_conda/envs
> LANG=en_ZA.UTF-8
> MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/apps/etc/modulefiles
> LOADEDMODULES=
> KDEDIRS=/usr
> PS1=(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3)
> \[\e[1;31;40m\][\u@\h \w]$\[\e[0m\]
> SELINUX_LEVEL_REQUESTED=
> HISTCONTROL=ignoredups
> SHLVL=1
> HOME=/root
> CONDA_PS1_BACKUP=\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\]
> PERL_LOCAL_LIB_ROOT=:/root/perl5
> LOGNAME=root
> QTLIB=/usr/lib64/qt-3.3/lib
> SSH_CONNECTION=10.55.40.3 55438 10.55.40.1 22
> MODULESHOME=/usr/share/Modules
> CONDA_DEFAULT_ENV=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
> LESSOPEN=||/usr/bin/lesspipe.sh %s
> XDG_RUNTIME_DIR=/run/user/0
> QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
> PERL_MM_OPT=INSTALL_BASE=/root/perl5
> XAUTHORITY=/tmp/.Xauthority.root
> BASH_FUNC_module()=() {  eval `/usr/bin/modulecmd bash $*`
> }
> _=/usr/bin/env
> (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
> /home/.galaxy/tooldeps/_conda/envs]$
>
>
> ------------------------------------------------------------------------
> *From:* Björn Grüning <[hidden email]>
> *Sent:* 10 July 2018 08:38:15
> *To:* Van Wageningen, GERHARD [[hidden email]];
> [hidden email]
> *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
> environment
> Hi,
>
> can you do:
>
>    . /home/.galaxy/tooldeps/_conda/bin/activate
> '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
>
> And see if you can execute trim_galore from the commandline and get the
> help?
>
> Ciao,
> Bjoern
>
> Am 10.07.2018 um 08:34 schrieb Van Wageningen, GERHARD [[hidden email]]:
>> Hi Bjoern, thanks for the pointer ... We are running the default
>> dependency_resolvers_conf.xml now and that, along with the symlinks hint
>> has helped with a lot of the tool dep. issues.  But there is still a
>> pathing issue we are stuck on.
>>
>> Take for example the trim_galore tool.
>>
>> The error is
>>
>> /home/.galaxy/database/jobs_directory/007/7480/tool_script.sh: line 25:
>> trim_galore: command not found
>>
>> And the script is:
>>
>> #!/bin/bash
>>
>> # The following block can be used by the job system
>> # to ensure this script is runnable before actually attempting
>> # to run it.
>> if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
>>      exit 42
>> fi
>> [ "$CONDA_DEFAULT_ENV" =
>> "/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3" ] ||
>> MAX_TRIES=3
>> COUNT=0
>> while [ $COUNT -lt $MAX_TRIES ]; do
>>      . /home/.galaxy/tooldeps/_conda/bin/activate
>> '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3' >
>> conda_activate.log 2>&1
>>      if [ $? -eq 0 ];then
>>          break
>>      else
>>          let COUNT=COUNT+1
>>          if [ $COUNT -eq $MAX_TRIES ];then
>>              echo "Failed to activate conda environment! Error was:"
>>              cat conda_activate.log
>>              exit 1
>>          fi
>>          sleep 10s
>>      fi
>> done ; trim_galore --version >
>> /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7477 2>&1; ln -s
>> '/home/.galaxy/database/files/013/dataset_13139.dat' input_1.fastq &&  
>> trim_galore  --phred33    --output_dir ./      input_1.fastq  
>> --dont_gzip  && if [ -f input_1_trimmed.fq.gz ] ; then mv
>> input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f
>> input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ;
>> fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz
>> input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv
>> input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f
>> input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz
>> input_2_unpaired_2.fq ; fi
>>
>>
>>
>> In fact most of the tools do this post-upgrade - where they cannot find
>> a file.
>>
>> Here is the trace from hisat2 - it fails in a similar way so we conclude
>> that there is a common underlying fault here that is affecting the
>> pathing of the scripts.
>>
>> Any ideas how we should go about finding this error?
>>
>> Thanks, Gerhard
>>
>> PS Here is the hisat2 output.
>>
>> #!/bin/bash
>>
>> # The following block can be used by the job system
>>
>> # to ensure this script is runnable before actually attempting
>>
>> # to run it.
>>
>> if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
>>
>>      exit 42
>>
>> fi
>>
>> [ "$CONDA_DEFAULT_ENV" =
>> "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426"
>> ] ||
>>
>> MAX_TRIES=3
>>
>> COUNT=0
>>
>> while [ $COUNT -lt $MAX_TRIES ]; do
>>
>>      . /home/.galaxy/tooldeps/_conda/bin/activate
>> '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
>>  > conda_activate.log 2>&1
>>
>>      if [ $? -eq 0 ];then
>>
>>          break
>>
>>      else
>>
>>          let COUNT=COUNT+1
>>
>>          if [ $COUNT -eq $MAX_TRIES ];then
>>
>>              echo "Failed to activate conda environment! Error was:"
>>
>>              cat conda_activate.log
>>
>>              exit 1
>>
>>          fi
>>
>>          sleep 10s
>>
>>      fi
>>
>> done ; [ "$CONDA_DEFAULT_ENV" =
>> "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426"
>> ] ||
>>
>> MAX_TRIES=3
>>
>> COUNT=0
>>
>> while [ $COUNT -lt $MAX_TRIES ]; do
>>
>>      . /home/.galaxy/tooldeps/_conda/bin/activate
>> '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
>>  > conda_activate.log 2>&1
>>
>>      if [ $? -eq 0 ];then
>>
>>          break
>>
>>      else
>>
>>          let COUNT=COUNT+1
>>
>>          if [ $COUNT -eq $MAX_TRIES ];then
>>
>>              echo "Failed to activate conda environment! Error was:"
>>
>>              cat conda_activate.log
>>
>>              exit 1
>>
>>          fi
>>
>>          sleep 10s
>>
>>      fi
>>
>> done ; hisat2 --version >
>> /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7484 2>&1; set -o | grep -q
>> pipefail && set -o pipefail;   ln -s
>> '/home/.galaxy/database/files/013/dataset_13248.dat' genome.fa &&
>> _hisat2-build_ -p ${GALAXY_SLOTS:-1} genome.fa genome &&        ln -f -s
>> '/home/.galaxy/database/files/013/dataset_13238.dat' input_f.fastq &&  
>> ln -f -s '/home/.galaxy/database/files/013/dataset_13243.dat'
>> input_r.fastq &&     hisat2  -p ${GALAXY_SLOTS:-1}  -x 'genome'     -1
>> 'input_f.fastq' -2 'input_r.fastq'                               |
>> samtools sort - -@ ${GALAXY_SLOTS:-1} -l 6 -o
>> '/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat'
>>
>> The job fails when it cannot find “hisat2-build”.
>>
>> Fatal error: Exit code 127 ()
>>
>> /home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41:
>> hisat2-build: command not found
>>
>> The PATH variable should be exported with installation
>> (/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh):
>>
>> PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH;
>> export PATH
>>
>> HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43;
>> export HISAT2_ROOT_DIR
>>
>> HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43;
>> export HISAT_ROOT_DIR
>>
>> The conda environment with dependencies seems to be there:
>>
>> /home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin
>>
>>
>>
>>
>> Björn Grüning <[hidden email]>;
>> [hidden email]
>>
>> ------------------------------------------------------------------------
>> *From:* Björn Grüning <[hidden email]>
>> *Sent:* 05 July 2018 22:00:58
>> *To:* Van Wageningen, GERHARD [[hidden email]];
>> [hidden email]
>> *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
>> environment
>> Hi Gerhard,
>>
>> it seems your tool is picking up the old tool_dependency version and not
>> the conda version of python.
>>
>> Have a look at
>> https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample 
>
>>
>> <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
>>        
>> galaxyproject/galaxy
>> <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
>> github.com
>> galaxy - Data intensive science for everyone.
>>
>>
>>
>> to configure the order of dependency resolution in Galaxy.
>>
>> Cheers,
>> Bjoern
>>
>>> 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:
>>>
>>>
>>> Thanks, hopefully someone has seen this before ...
>>>
>>>
>>> regards, Gerhard
>>>
>>>
>>>
>>> [program:web]
>>> command         = uwsgi --plugin python --virtualenv /home/.galaxy/.venv
>>> --ini-paste /home/.galaxy/config/galaxy.ini
>>> directory       = /home/.galaxy
>>> umask           = 022
>>> autostart       = true
>>> autorestart     = true
>>> startsecs       = 10
>>> user            = galaxy
>>> numprocs        = 1
>>> stopsignal      = INT
>>>
>>> [program:handler]
>>> command         = python ./scripts/galaxy-main -c
>>> /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s
>>> directory       = /home/.galaxy
>>> process_name    = handler%(process_num)s
>>> numprocs        = 1
>>> umask           = 022
>>> autostart       = true
>>> autorestart     = true
>>> startsecs       = 10
>>> user            = galaxy
>>> environment     =
>>> VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/"
>>> stdout_logfile  = /home/.galaxy/handler%(process_num)s.log
>>> redirect_stderr = true
>>>
>>> [group:galaxy]
>>> programs        = handler, web
>>>
>>> <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 >
>>>
>>>
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>>> Please keep all replies on the list by using "reply all"
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Re: Conda problems: Failed to activate conda environment

Van Wageningen, GERHARD [gerhardv@sun.ac.za]

So those files are "just not there" due to a faulty install?  And the repair is to delete the __toolname.x.x.x folders from the _conda/envs folder and force conda to reinstall them?


Where can I look for the channel priorities and is there a standard rule for them?


Thanks for your input - must appreciated!


gerhard


From: Björn Grüning <[hidden email]>
Sent: 10 July 2018 08:49:04
To: Van Wageningen, GERHARD [[hidden email]]; [hidden email]
Subject: Re: [galaxy-dev] Conda problems: Failed to activate conda environment
 
Which means that your conda envs are not what they are supposed to be.

You can fix this by removing the folder and let Galaxy re-created them,
but you should figure out why they are "empty". Maybe a wrong channel
priority or network issues during installation?

Hope that helps.
You could also from insite the env, do a `conda install ...`

> Hi - tx for (fast) reply.  Ok ... with this result ...
>
>
> (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
> /home/.galaxy/tooldeps/_conda/envs]$ trim_galore --version
> -bash: trim_galore: command not found
>
> Environment is:
>
> (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
> /home/.galaxy/tooldeps/_conda/envs]$ env
> XDG_SESSION_ID=45352
> HOSTNAME=storage1.hpc
> SELINUX_ROLE_REQUESTED=
> TERM=xterm-256color
> SHELL=/bin/bash
> HISTSIZE=1000
> SSH_CLIENT=10.55.40.3 55438 22
> PERL5LIB=/root/perl5/lib/perl5:/usr/local/lib/perl5:
> SELINUX_USE_CURRENT_RANGE=
> QTDIR=/usr/lib64/qt-3.3
> OLDPWD=/home/.galaxy/tooldeps/_conda/envs/__hisat2@2.1.0
> QTINC=/usr/lib64/qt-3.3/include
> PERL_MB_OPT=--install_base /root/perl5
> SSH_TTY=/dev/pts/2
> QT_GRAPHICSSYSTEM_CHECKED=1
> USER=root
> LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
> MAIL=/var/spool/mail/root
> PATH=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3/bin:/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
> CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
> CONDA_PREFIX=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
> CONDA=/home/.galaxy/tooldeps/_conda
> PWD=/home/.galaxy/tooldeps/_conda/envs
> LANG=en_ZA.UTF-8
> MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/apps/etc/modulefiles
> LOADEDMODULES=
> KDEDIRS=/usr
> PS1=(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3)
> \[\e[1;31;40m\][\u@\h \w]$\[\e[0m\]
> SELINUX_LEVEL_REQUESTED=
> HISTCONTROL=ignoredups
> SHLVL=1
> HOME=/root
> CONDA_PS1_BACKUP=\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\]
> PERL_LOCAL_LIB_ROOT=:/root/perl5
> LOGNAME=root
> QTLIB=/usr/lib64/qt-3.3/lib
> SSH_CONNECTION=10.55.40.3 55438 10.55.40.1 22
> MODULESHOME=/usr/share/Modules
> CONDA_DEFAULT_ENV=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
> LESSOPEN=||/usr/bin/lesspipe.sh %s
> XDG_RUNTIME_DIR=/run/user/0
> QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
> PERL_MM_OPT=INSTALL_BASE=/root/perl5
> XAUTHORITY=/tmp/.Xauthority.root
> BASH_FUNC_module()=() {  eval `/usr/bin/modulecmd bash $*`
> }
> _=/usr/bin/env
> (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
> /home/.galaxy/tooldeps/_conda/envs]$
>
>
> ------------------------------------------------------------------------
> *From:* Björn Grüning <[hidden email]>
> *Sent:* 10 July 2018 08:38:15
> *To:* Van Wageningen, GERHARD [[hidden email]];
> [hidden email]
> *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
> environment
> Hi,
>
> can you do:
>
>    . /home/.galaxy/tooldeps/_conda/bin/activate
> '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
>
> And see if you can execute trim_galore from the commandline and get the
> help?
>
> Ciao,
> Bjoern
>
> Am 10.07.2018 um 08:34 schrieb Van Wageningen, GERHARD [[hidden email]]:
>> Hi Bjoern, thanks for the pointer ... We are running the default
>> dependency_resolvers_conf.xml now and that, along with the symlinks hint
>> has helped with a lot of the tool dep. issues.  But there is still a
>> pathing issue we are stuck on.
>>
>> Take for example the trim_galore tool.
>>
>> The error is
>>
>> /home/.galaxy/database/jobs_directory/007/7480/tool_script.sh: line 25:
>> trim_galore: command not found
>>
>> And the script is:
>>
>> #!/bin/bash
>>
>> # The following block can be used by the job system
>> # to ensure this script is runnable before actually attempting
>> # to run it.
>> if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
>>      exit 42
>> fi
>> [ "$CONDA_DEFAULT_ENV" =
>> "/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3" ] ||
>> MAX_TRIES=3
>> COUNT=0
>> while [ $COUNT -lt $MAX_TRIES ]; do
>>      . /home/.galaxy/tooldeps/_conda/bin/activate
>> '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3' >
>> conda_activate.log 2>&1
>>      if [ $? -eq 0 ];then
>>          break
>>      else
>>          let COUNT=COUNT+1
>>          if [ $COUNT -eq $MAX_TRIES ];then
>>              echo "Failed to activate conda environment! Error was:"
>>              cat conda_activate.log
>>              exit 1
>>          fi
>>          sleep 10s
>>      fi
>> done ; trim_galore --version >
>> /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7477 2>&1; ln -s
>> '/home/.galaxy/database/files/013/dataset_13139.dat' input_1.fastq && 
>> trim_galore  --phred33    --output_dir ./      input_1.fastq 
>> --dont_gzip  && if [ -f input_1_trimmed.fq.gz ] ; then mv
>> input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f
>> input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ;
>> fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz
>> input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv
>> input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f
>> input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz
>> input_2_unpaired_2.fq ; fi
>>
>>
>>
>> In fact most of the tools do this post-upgrade - where they cannot find
>> a file.
>>
>> Here is the trace from hisat2 - it fails in a similar way so we conclude
>> that there is a common underlying fault here that is affecting the
>> pathing of the scripts.
>>
>> Any ideas how we should go about finding this error?
>>
>> Thanks, Gerhard
>>
>> PS Here is the hisat2 output.
>>
>> #!/bin/bash
>>
>> # The following block can be used by the job system
>>
>> # to ensure this script is runnable before actually attempting
>>
>> # to run it.
>>
>> if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
>>
>>      exit 42
>>
>> fi
>>
>> [ "$CONDA_DEFAULT_ENV" =
>> "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426"
>> ] ||
>>
>> MAX_TRIES=3
>>
>> COUNT=0
>>
>> while [ $COUNT -lt $MAX_TRIES ]; do
>>
>>      . /home/.galaxy/tooldeps/_conda/bin/activate
>> '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
>>  > conda_activate.log 2>&1
>>
>>      if [ $? -eq 0 ];then
>>
>>          break
>>
>>      else
>>
>>          let COUNT=COUNT+1
>>
>>          if [ $COUNT -eq $MAX_TRIES ];then
>>
>>              echo "Failed to activate conda environment! Error was:"
>>
>>              cat conda_activate.log
>>
>>              exit 1
>>
>>          fi
>>
>>          sleep 10s
>>
>>      fi
>>
>> done ; [ "$CONDA_DEFAULT_ENV" =
>> "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426"
>> ] ||
>>
>> MAX_TRIES=3
>>
>> COUNT=0
>>
>> while [ $COUNT -lt $MAX_TRIES ]; do
>>
>>      . /home/.galaxy/tooldeps/_conda/bin/activate
>> '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
>>  > conda_activate.log 2>&1
>>
>>      if [ $? -eq 0 ];then
>>
>>          break
>>
>>      else
>>
>>          let COUNT=COUNT+1
>>
>>          if [ $COUNT -eq $MAX_TRIES ];then
>>
>>              echo "Failed to activate conda environment! Error was:"
>>
>>              cat conda_activate.log
>>
>>              exit 1
>>
>>          fi
>>
>>          sleep 10s
>>
>>      fi
>>
>> done ; hisat2 --version >
>> /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7484 2>&1; set -o | grep -q
>> pipefail && set -o pipefail;   ln -s
>> '/home/.galaxy/database/files/013/dataset_13248.dat' genome.fa &&
>> _hisat2-build_ -p ${GALAXY_SLOTS:-1} genome.fa genome &&        ln -f -s
>> '/home/.galaxy/database/files/013/dataset_13238.dat' input_f.fastq && 
>> ln -f -s '/home/.galaxy/database/files/013/dataset_13243.dat'
>> input_r.fastq &&     hisat2  -p ${GALAXY_SLOTS:-1}  -x 'genome'     -1
>> 'input_f.fastq' -2 'input_r.fastq'                               |
>> samtools sort - -@ ${GALAXY_SLOTS:-1} -l 6 -o
>> '/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat'
>>
>> The job fails when it cannot find “hisat2-build”.
>>
>> Fatal error: Exit code 127 ()
>>
>> /home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41:
>> hisat2-build: command not found
>>
>> The PATH variable should be exported with installation
>> (/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh):
>>
>> PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH;
>> export PATH
>>
>> HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43;
>> export HISAT2_ROOT_DIR
>>
>> HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43;
>> export HISAT_ROOT_DIR
>>
>> The conda environment with dependencies seems to be there:
>>
>> /home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin
>>
>>
>>
>>
>> Björn Grüning <[hidden email]>;
>> [hidden email]
>>
>> ------------------------------------------------------------------------
>> *From:* Björn Grüning <[hidden email]>
>> *Sent:* 05 July 2018 22:00:58
>> *To:* Van Wageningen, GERHARD [[hidden email]];
>> [hidden email]
>> *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
>> environment
>> Hi Gerhard,
>>
>> it seems your tool is picking up the old tool_dependency version and not
>> the conda version of python.
>>
>> Have a look at
>> https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample
>
>>
>> <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
>>       
>> galaxyproject/galaxy
>> <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
>> github.com
>> galaxy - Data intensive science for everyone.
>>
>>
>>
>> to configure the order of dependency resolution in Galaxy.
>>
>> Cheers,
>> Bjoern
>>
>>> 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:
>>>
>>>
>>> Thanks, hopefully someone has seen this before ...
>>>
>>>
>>> regards, Gerhard
>>>
>>>
>>>
>>> [program:web]
>>> command         = uwsgi --plugin python --virtualenv /home/.galaxy/.venv
>>> --ini-paste /home/.galaxy/config/galaxy.ini
>>> directory       = /home/.galaxy
>>> umask           = 022
>>> autostart       = true
>>> autorestart     = true
>>> startsecs       = 10
>>> user            = galaxy
>>> numprocs        = 1
>>> stopsignal      = INT
>>>
>>> [program:handler]
>>> command         = python ./scripts/galaxy-main -c
>>> /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s
>>> directory       = /home/.galaxy
>>> process_name    = handler%(process_num)s
>>> numprocs        = 1
>>> umask           = 022
>>> autostart       = true
>>> autorestart     = true
>>> startsecs       = 10
>>> user            = galaxy
>>> environment     =
>>> VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/"
>>> stdout_logfile  = /home/.galaxy/handler%(process_num)s.log
>>> redirect_stderr = true
>>>
>>> [group:galaxy]
>>> programs        = handler, web
>>>
>>> <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 >
>>>
>>>
>>> ___________________________________________________________
>>> 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/
>>>
>> <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 >
> <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 >

The integrity and confidentiality of this email is governed by these terms. Disclaimer
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule

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Re: Conda problems: Failed to activate conda environment

Björn Grüning-3


Am 10.07.2018 um 08:54 schrieb Van Wageningen, GERHARD [[hidden email]]:
> So those files are "just not there" due to a faulty install?

Seems so.
You can try for hisat as well.
The questions is why :(

> And the
> repair is to delete the __toolname.x.x.x folders from the _conda/envs
> folder and force conda to reinstall them?


Yes.

>
> Where can I look for the channel priorities and is there a standard rule
> for them?

https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L240

Cheers,
Bjoern

>
> Thanks for your input - must appreciated!
>
>
> gerhard
>
> ------------------------------------------------------------------------
> *From:* Björn Grüning <[hidden email]>
> *Sent:* 10 July 2018 08:49:04
> *To:* Van Wageningen, GERHARD [[hidden email]];
> [hidden email]
> *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
> environment
> Which means that your conda envs are not what they are supposed to be.
>
> You can fix this by removing the folder and let Galaxy re-created them,
> but you should figure out why they are "empty". Maybe a wrong channel
> priority or network issues during installation?
>
> Hope that helps.
> You could also from insite the env, do a `conda install ...`
>
>> Hi - tx for (fast) reply.  Ok ... with this result ...
>>
>>
>> (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
>> /home/.galaxy/tooldeps/_conda/envs]$ trim_galore --version
>> -bash: trim_galore: command not found
>>
>> Environment is:
>>
>> (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
>> /home/.galaxy/tooldeps/_conda/envs]$ env
>> XDG_SESSION_ID=45352
>> HOSTNAME=storage1.hpc
>> SELINUX_ROLE_REQUESTED=
>> TERM=xterm-256color
>> SHELL=/bin/bash
>> HISTSIZE=1000
>> SSH_CLIENT=10.55.40.3 55438 22
>> PERL5LIB=/root/perl5/lib/perl5:/usr/local/lib/perl5:
>> SELINUX_USE_CURRENT_RANGE=
>> QTDIR=/usr/lib64/qt-3.3
>> OLDPWD=/home/.galaxy/tooldeps/_conda/envs/__hisat2@2.1.0
>> QTINC=/usr/lib64/qt-3.3/include
>> PERL_MB_OPT=--install_base /root/perl5
>> SSH_TTY=/dev/pts/2
>> QT_GRAPHICSSYSTEM_CHECKED=1
>> USER=root
>> LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
>> MAIL=/var/spool/mail/root
>> PATH=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3/bin:/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
>> CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
>> CONDA_PREFIX=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
>> CONDA=/home/.galaxy/tooldeps/_conda
>> PWD=/home/.galaxy/tooldeps/_conda/envs
>> LANG=en_ZA.UTF-8
>> MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/apps/etc/modulefiles
>> LOADEDMODULES=
>> KDEDIRS=/usr
>> PS1=(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3)
>> \[\e[1;31;40m\][\u@\h \w]$\[\e[0m\]
>> SELINUX_LEVEL_REQUESTED=
>> HISTCONTROL=ignoredups
>> SHLVL=1
>> HOME=/root
>> CONDA_PS1_BACKUP=\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\]
>> PERL_LOCAL_LIB_ROOT=:/root/perl5
>> LOGNAME=root
>> QTLIB=/usr/lib64/qt-3.3/lib
>> SSH_CONNECTION=10.55.40.3 55438 10.55.40.1 22
>> MODULESHOME=/usr/share/Modules
>> CONDA_DEFAULT_ENV=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
>> LESSOPEN=||/usr/bin/lesspipe.sh %s
>> XDG_RUNTIME_DIR=/run/user/0
>> QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
>> PERL_MM_OPT=INSTALL_BASE=/root/perl5
>> XAUTHORITY=/tmp/.Xauthority.root
>> BASH_FUNC_module()=() {  eval `/usr/bin/modulecmd bash $*`
>> }
>> _=/usr/bin/env
>> (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
>> /home/.galaxy/tooldeps/_conda/envs]$
>>
>>
>> ------------------------------------------------------------------------
>> *From:* Björn Grüning <[hidden email]>
>> *Sent:* 10 July 2018 08:38:15
>> *To:* Van Wageningen, GERHARD [[hidden email]];
>> [hidden email]
>> *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
>> environment
>> Hi,
>>
>> can you do:
>>
>>    . /home/.galaxy/tooldeps/_conda/bin/activate
>> '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
>>
>> And see if you can execute trim_galore from the commandline and get the
>> help?
>>
>> Ciao,
>> Bjoern
>>
>> Am 10.07.2018 um 08:34 schrieb Van Wageningen, GERHARD [[hidden email]]:
>>> Hi Bjoern, thanks for the pointer ... We are running the default
>>> dependency_resolvers_conf.xml now and that, along with the symlinks hint
>>> has helped with a lot of the tool dep. issues.  But there is still a
>>> pathing issue we are stuck on.
>>>
>>> Take for example the trim_galore tool.
>>>
>>> The error is
>>>
>>> /home/.galaxy/database/jobs_directory/007/7480/tool_script.sh: line 25:
>>> trim_galore: command not found
>>>
>>> And the script is:
>>>
>>> #!/bin/bash
>>>
>>> # The following block can be used by the job system
>>> # to ensure this script is runnable before actually attempting
>>> # to run it.
>>> if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
>>>      exit 42
>>> fi
>>> [ "$CONDA_DEFAULT_ENV" =
>>> "/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3" ] ||
>>> MAX_TRIES=3
>>> COUNT=0
>>> while [ $COUNT -lt $MAX_TRIES ]; do
>>>      . /home/.galaxy/tooldeps/_conda/bin/activate
>>> '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3' >
>>> conda_activate.log 2>&1
>>>      if [ $? -eq 0 ];then
>>>          break
>>>      else
>>>          let COUNT=COUNT+1
>>>          if [ $COUNT -eq $MAX_TRIES ];then
>>>              echo "Failed to activate conda environment! Error was:"
>>>              cat conda_activate.log
>>>              exit 1
>>>          fi
>>>          sleep 10s
>>>      fi
>>> done ; trim_galore --version >
>>> /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7477 2>&1; ln -s
>>> '/home/.galaxy/database/files/013/dataset_13139.dat' input_1.fastq &&  
>>> trim_galore  --phred33    --output_dir ./      input_1.fastq  
>>> --dont_gzip  && if [ -f input_1_trimmed.fq.gz ] ; then mv
>>> input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f
>>> input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ;
>>> fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz
>>> input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv
>>> input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f
>>> input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz
>>> input_2_unpaired_2.fq ; fi
>>>
>>>
>>>
>>> In fact most of the tools do this post-upgrade - where they cannot find
>>> a file.
>>>
>>> Here is the trace from hisat2 - it fails in a similar way so we conclude
>>> that there is a common underlying fault here that is affecting the
>>> pathing of the scripts.
>>>
>>> Any ideas how we should go about finding this error?
>>>
>>> Thanks, Gerhard
>>>
>>> PS Here is the hisat2 output.
>>>
>>> #!/bin/bash
>>>
>>> # The following block can be used by the job system
>>>
>>> # to ensure this script is runnable before actually attempting
>>>
>>> # to run it.
>>>
>>> if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
>>>
>>>      exit 42
>>>
>>> fi
>>>
>>> [ "$CONDA_DEFAULT_ENV" =
>>> "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426"
>>> ] ||
>>>
>>> MAX_TRIES=3
>>>
>>> COUNT=0
>>>
>>> while [ $COUNT -lt $MAX_TRIES ]; do
>>>
>>>      . /home/.galaxy/tooldeps/_conda/bin/activate
>>> '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
>>>  > conda_activate.log 2>&1
>>>
>>>      if [ $? -eq 0 ];then
>>>
>>>          break
>>>
>>>      else
>>>
>>>          let COUNT=COUNT+1
>>>
>>>          if [ $COUNT -eq $MAX_TRIES ];then
>>>
>>>              echo "Failed to activate conda environment! Error was:"
>>>
>>>              cat conda_activate.log
>>>
>>>              exit 1
>>>
>>>          fi
>>>
>>>          sleep 10s
>>>
>>>      fi
>>>
>>> done ; [ "$CONDA_DEFAULT_ENV" =
>>> "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426"
>>> ] ||
>>>
>>> MAX_TRIES=3
>>>
>>> COUNT=0
>>>
>>> while [ $COUNT -lt $MAX_TRIES ]; do
>>>
>>>      . /home/.galaxy/tooldeps/_conda/bin/activate
>>> '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
>>>  > conda_activate.log 2>&1
>>>
>>>      if [ $? -eq 0 ];then
>>>
>>>          break
>>>
>>>      else
>>>
>>>          let COUNT=COUNT+1
>>>
>>>          if [ $COUNT -eq $MAX_TRIES ];then
>>>
>>>              echo "Failed to activate conda environment! Error was:"
>>>
>>>              cat conda_activate.log
>>>
>>>              exit 1
>>>
>>>          fi
>>>
>>>          sleep 10s
>>>
>>>      fi
>>>
>>> done ; hisat2 --version >
>>> /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7484 2>&1; set -o | grep -q
>>> pipefail && set -o pipefail;   ln -s
>>> '/home/.galaxy/database/files/013/dataset_13248.dat' genome.fa &&
>>> _hisat2-build_ -p ${GALAXY_SLOTS:-1} genome.fa genome &&        ln -f -s
>>> '/home/.galaxy/database/files/013/dataset_13238.dat' input_f.fastq &&  
>>> ln -f -s '/home/.galaxy/database/files/013/dataset_13243.dat'
>>> input_r.fastq &&     hisat2  -p ${GALAXY_SLOTS:-1}  -x 'genome'     -1
>>> 'input_f.fastq' -2 'input_r.fastq'                               |
>>> samtools sort - -@ ${GALAXY_SLOTS:-1} -l 6 -o
>>> '/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat'
>>>
>>> The job fails when it cannot find “hisat2-build”.
>>>
>>> Fatal error: Exit code 127 ()
>>>
>>> /home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41:
>>> hisat2-build: command not found
>>>
>>> The PATH variable should be exported with installation
>>> (/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh):
>>>
>>> PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH;
>>> export PATH
>>>
>>> HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43;
>>> export HISAT2_ROOT_DIR
>>>
>>> HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43;
>>> export HISAT_ROOT_DIR
>>>
>>> The conda environment with dependencies seems to be there:
>>>
>>> /home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin
>>>
>>>
>>>
>>>
>>> Björn Grüning <[hidden email]>;
>>> [hidden email]
>>>
>>> ------------------------------------------------------------------------
>>> *From:* Björn Grüning <[hidden email]>
>>> *Sent:* 05 July 2018 22:00:58
>>> *To:* Van Wageningen, GERHARD [[hidden email]];
>>> [hidden email]
>>> *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
>>> environment
>>> Hi Gerhard,
>>>
>>> it seems your tool is picking up the old tool_dependency version and not
>>> the conda version of python.
>>>
>>> Have a look at
>>> https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample 
>
>>
>>>
>>> <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
>>>        
>>> galaxyproject/galaxy
>>> <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
>>> github.com
>>> galaxy - Data intensive science for everyone.
>>>
>>>
>>>
>>> to configure the order of dependency resolution in Galaxy.
>>>
>>> Cheers,
>>> Bjoern
>>>
>>>> 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:
>>>>
>>>>
>>>> Thanks, hopefully someone has seen this before ...
>>>>
>>>>
>>>> regards, Gerhard
>>>>
>>>>
>>>>
>>>> [program:web]
>>>> command         = uwsgi --plugin python --virtualenv /home/.galaxy/.venv
>>>> --ini-paste /home/.galaxy/config/galaxy.ini
>>>> directory       = /home/.galaxy
>>>> umask           = 022
>>>> autostart       = true
>>>> autorestart     = true
>>>> startsecs       = 10
>>>> user            = galaxy
>>>> numprocs        = 1
>>>> stopsignal      = INT
>>>>
>>>> [program:handler]
>>>> command         = python ./scripts/galaxy-main -c
>>>> /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s
>>>> directory       = /home/.galaxy
>>>> process_name    = handler%(process_num)s
>>>> numprocs        = 1
>>>> umask           = 022
>>>> autostart       = true
>>>> autorestart     = true
>>>> startsecs       = 10
>>>> user            = galaxy
>>>> environment     =
>>>> VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/"
>>>> stdout_logfile  = /home/.galaxy/handler%(process_num)s.log
>>>> redirect_stderr = true
>>>>
>>>> [group:galaxy]
>>>> programs        = handler, web
>>>>
>>>> <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 >
>>>>
>>>>
>>>> ___________________________________________________________
>>>> 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/
>>>>
>>> <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 >
>> <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 >
> <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 >
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Re: Conda problems: Failed to activate conda environment

Van Wageningen, GERHARD [gerhardv@sun.ac.za]

Hi - We have been trying to clean up the Galaxy tool deps ... have this interesting log as a result.  Getting a lot of these:

"DependencyException: Conda dependency seemingly installed but failed to build job environment."

I am curious about the way files play in different locations in Galaxy:  For example when tools are installed - Bowtie2, hisat2 or trim-galore ... the same file exists in _conda/pkgs, _conda/envs/__too.xx and _conda/envs/mulled-1-xxx

Is something dynamically pathing the executables into environment variables on the fly when a tool is launched?

Anyway - here's the interesting log.  I think we are going to have to start from the beginning and redo our galaxy.

Tx
Gerhard


galaxy.tools.deps DEBUG 2018-07-11 09:00:44,989 Using dependency bowtie2 version 0d9cd7487cc9 of type galaxy_package
galaxy.tools.deps DEBUG 2018-07-11 09:00:45,047 Using dependency samtools version 1.8 of type conda
galaxy.tools.deps.conda_util DEBUG 2018-07-11 09:00:45,113 Executing command: /home/.galaxy/tooldeps/_conda/bin/conda --debug list --name __samtools@1.8 --export > '/scratch2/galaxy/tmp/jobdepsE4Lr1n08340d69faa2de38b5657876909fd6669c7f31431857f443b6be50341be135e5/__samtools@1.8'
galaxy.tools.deps.conda_util DEBUG 2018-07-11 09:00:59,860 Executing command: /home/.galaxy/tooldeps/_conda/bin/conda --debug create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --unknown --offline --prefix /home/.galaxy/database/jobs_directory/007/7553/conda-env --file /scratch2/galaxy/tmp/jobdepsE4Lr1n08340d69faa2de38b5657876909fd6669c7f31431857f443b6be50341be135e5/__samtools@1.8
Fetching package metadata ...
.Solving package specifications: ....


UnsatisfiableError: The following specifications were found to be in conflict:
  - bzip2 1.0.6 3
  - krb5 1.13.2 0
Use "conda info <package>" to see the dependencies for each package.


galaxy.tools.deps.conda_util DEBUG 2018-07-11 09:01:53,255 Executing command: /home/.galaxy/tooldeps/_conda/bin/conda --debug clean --tarballs -y
Cache location: /home/.galaxy/tooldeps/_conda/pkgs
Will remove the following tarballs:

/home/.galaxy/tooldeps/_conda/pkgs
----------------------------------
r-plogr-0.2.0-r341h6115d3f_0.tar.bz2          17 KB
r-getopt-1.20.2-r3.4.1_0.tar.bz2              29 KB
libpng-1.6.28-2.tar.bz2                      302 KB
libtiff-4.0.7-1.tar.bz2                      488 KB
r-withr-2.1.1-r3.4.1_0.tar.bz2               130 KB
r-stringi-1.2.3-r341_0.tar.bz2               704 KB
libxml2-2.9.5-1.tar.bz2                      5.0 MB
r-nlme-3.1_131-r3.4.1_0.tar.bz2              2.2 MB
r-rcpparmadillo-0.8.500.0-r3.4.1_0.tar.bz2     1.2 MB
r-gtools-3.8.1-r341_0.tar.bz2                265 KB
cairo-1.14.6-5.tar.bz2                       1.2 MB
r-ggplot2-3.0.0-r341h6115d3f_0.tar.bz2       3.0 MB
freetype-2.7-2.tar.bz2                       2.8 MB
r-stringr-1.3.1-r341_0.tar.bz2               164 KB
r-rcpp-0.12.16-r3.4.1_0.tar.bz2              3.3 MB
r-mgcv-1.8_24-r341_0.tar.bz2                 2.4 MB
r-rjson-0.2.15-r3.4.1_0.tar.bz2              123 KB

---------------------------------------------------
Total:                                      23.4 MB

Removing r-plogr-0.2.0-r341h6115d3f_0.tar.bz2
Removing r-getopt-1.20.2-r3.4.1_0.tar.bz2
Removing libpng-1.6.28-2.tar.bz2
Removing libtiff-4.0.7-1.tar.bz2
Removing r-withr-2.1.1-r3.4.1_0.tar.bz2
Removing r-stringi-1.2.3-r341_0.tar.bz2
Removing libxml2-2.9.5-1.tar.bz2
Removing r-nlme-3.1_131-r3.4.1_0.tar.bz2
Removing r-rcpparmadillo-0.8.500.0-r3.4.1_0.tar.bz2
Removing r-gtools-3.8.1-r341_0.tar.bz2
Removing cairo-1.14.6-5.tar.bz2
Removing r-ggplot2-3.0.0-r341h6115d3f_0.tar.bz2
Removing freetype-2.7-2.tar.bz2
Removing r-stringr-1.3.1-r341_0.tar.bz2
Removing r-rcpp-0.12.16-r3.4.1_0.tar.bz2
Removing r-mgcv-1.8_24-r341_0.tar.bz2
Removing r-rjson-0.2.15-r3.4.1_0.tar.bz2
galaxy.jobs.runners ERROR 2018-07-11 09:01:55,876 (7553) Failure preparing job
Traceback (most recent call last):
  File "/home/.galaxy/lib/galaxy/jobs/runners/__init__.py", line 192, in prepare_job
    job_wrapper.prepare()
  File "/home/.galaxy/lib/galaxy/jobs/__init__.py", line 869, in prepare
    self.dependency_shell_commands = self.tool.build_dependency_shell_commands(job_directory=self.working_directory)
  File "/home/.galaxy/lib/galaxy/tools/__init__.py", line 1556, in build_dependency_shell_commands
    tool_instance=self
  File "/home/.galaxy/lib/galaxy/tools/deps/__init__.py", line 113, in dependency_shell_commands
    return [dependency.shell_commands() for dependency in ordered_dependencies]
  File "/home/.galaxy/lib/galaxy/tools/deps/resolvers/conda.py", line 469, in shell_commands
    self.build_environment()
  File "/home/.galaxy/lib/galaxy/tools/deps/resolvers/conda.py", line 464, in build_environment
    raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")
DependencyException: Conda dependency seemingly installed but failed to build job environment.
galaxy.jobs DEBUG 2018-07-11 09:01:56,213 fail(): Moved /home/.galaxy/database/jobs_directory/007/7553/galaxy_dataset_19326.dat to /home/.galaxy/database/files/013/dataset_13389.dat



From: Björn Grüning <[hidden email]>
Sent: 10 July 2018 08:56:37
To: Van Wageningen, GERHARD [[hidden email]]; [hidden email]
Subject: Re: [galaxy-dev] Conda problems: Failed to activate conda environment
 


Am 10.07.2018 um 08:54 schrieb Van Wageningen, GERHARD [[hidden email]]:
> So those files are "just not there" due to a faulty install?

Seems so.
You can try for hisat as well.
The questions is why :(

> And the
> repair is to delete the __toolname.x.x.x folders from the _conda/envs
> folder and force conda to reinstall them?


Yes.

>
> Where can I look for the channel priorities and is there a standard rule
> for them?

https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L240

Cheers,
Bjoern

>
> Thanks for your input - must appreciated!
>
>
> gerhard
>
> ------------------------------------------------------------------------
> *From:* Björn Grüning <[hidden email]>
> *Sent:* 10 July 2018 08:49:04
> *To:* Van Wageningen, GERHARD [[hidden email]];
> [hidden email]
> *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
> environment
> Which means that your conda envs are not what they are supposed to be.
>
> You can fix this by removing the folder and let Galaxy re-created them,
> but you should figure out why they are "empty". Maybe a wrong channel
> priority or network issues during installation?
>
> Hope that helps.
> You could also from insite the env, do a `conda install ...`
>
>> Hi - tx for (fast) reply.  Ok ... with this result ...
>>
>>
>> (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
>> /home/.galaxy/tooldeps/_conda/envs]$ trim_galore --version
>> -bash: trim_galore: command not found
>>
>> Environment is:
>>
>> (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
>> /home/.galaxy/tooldeps/_conda/envs]$ env
>> XDG_SESSION_ID=45352
>> HOSTNAME=storage1.hpc
>> SELINUX_ROLE_REQUESTED=
>> TERM=xterm-256color
>> SHELL=/bin/bash
>> HISTSIZE=1000
>> SSH_CLIENT=10.55.40.3 55438 22
>> PERL5LIB=/root/perl5/lib/perl5:/usr/local/lib/perl5:
>> SELINUX_USE_CURRENT_RANGE=
>> QTDIR=/usr/lib64/qt-3.3
>> OLDPWD=/home/.galaxy/tooldeps/_conda/envs/__hisat2@2.1.0
>> QTINC=/usr/lib64/qt-3.3/include
>> PERL_MB_OPT=--install_base /root/perl5
>> SSH_TTY=/dev/pts/2
>> QT_GRAPHICSSYSTEM_CHECKED=1
>> USER=root
>> LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
>> MAIL=/var/spool/mail/root
>> PATH=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3/bin:/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
>> CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
>> CONDA_PREFIX=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
>> CONDA=/home/.galaxy/tooldeps/_conda
>> PWD=/home/.galaxy/tooldeps/_conda/envs
>> LANG=en_ZA.UTF-8
>> MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/apps/etc/modulefiles
>> LOADEDMODULES=
>> KDEDIRS=/usr
>> PS1=(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3)
>> \[\e[1;31;40m\][\u@\h \w]$\[\e[0m\]
>> SELINUX_LEVEL_REQUESTED=
>> HISTCONTROL=ignoredups
>> SHLVL=1
>> HOME=/root
>> CONDA_PS1_BACKUP=\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\]
>> PERL_LOCAL_LIB_ROOT=:/root/perl5
>> LOGNAME=root
>> QTLIB=/usr/lib64/qt-3.3/lib
>> SSH_CONNECTION=10.55.40.3 55438 10.55.40.1 22
>> MODULESHOME=/usr/share/Modules
>> CONDA_DEFAULT_ENV=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
>> LESSOPEN=||/usr/bin/lesspipe.sh %s
>> XDG_RUNTIME_DIR=/run/user/0
>> QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
>> PERL_MM_OPT=INSTALL_BASE=/root/perl5
>> XAUTHORITY=/tmp/.Xauthority.root
>> BASH_FUNC_module()=() {  eval `/usr/bin/modulecmd bash $*`
>> }
>> _=/usr/bin/env
>> (/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
>> /home/.galaxy/tooldeps/_conda/envs]$
>>
>>
>> ------------------------------------------------------------------------
>> *From:* Björn Grüning <[hidden email]>
>> *Sent:* 10 July 2018 08:38:15
>> *To:* Van Wageningen, GERHARD [[hidden email]];
>> [hidden email]
>> *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
>> environment
>> Hi,
>>
>> can you do:
>>
>>    . /home/.galaxy/tooldeps/_conda/bin/activate
>> '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
>>
>> And see if you can execute trim_galore from the commandline and get the
>> help?
>>
>> Ciao,
>> Bjoern
>>
>> Am 10.07.2018 um 08:34 schrieb Van Wageningen, GERHARD [[hidden email]]:
>>> Hi Bjoern, thanks for the pointer ... We are running the default
>>> dependency_resolvers_conf.xml now and that, along with the symlinks hint
>>> has helped with a lot of the tool dep. issues.  But there is still a
>>> pathing issue we are stuck on.
>>>
>>> Take for example the trim_galore tool.
>>>
>>> The error is
>>>
>>> /home/.galaxy/database/jobs_directory/007/7480/tool_script.sh: line 25:
>>> trim_galore: command not found
>>>
>>> And the script is:
>>>
>>> #!/bin/bash
>>>
>>> # The following block can be used by the job system
>>> # to ensure this script is runnable before actually attempting
>>> # to run it.
>>> if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
>>>      exit 42
>>> fi
>>> [ "$CONDA_DEFAULT_ENV" =
>>> "/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3" ] ||
>>> MAX_TRIES=3
>>> COUNT=0
>>> while [ $COUNT -lt $MAX_TRIES ]; do
>>>      . /home/.galaxy/tooldeps/_conda/bin/activate
>>> '/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3' >
>>> conda_activate.log 2>&1
>>>      if [ $? -eq 0 ];then
>>>          break
>>>      else
>>>          let COUNT=COUNT+1
>>>          if [ $COUNT -eq $MAX_TRIES ];then
>>>              echo "Failed to activate conda environment! Error was:"
>>>              cat conda_activate.log
>>>              exit 1
>>>          fi
>>>          sleep 10s
>>>      fi
>>> done ; trim_galore --version >
>>> /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7477 2>&1; ln -s
>>> '/home/.galaxy/database/files/013/dataset_13139.dat' input_1.fastq && 
>>> trim_galore  --phred33    --output_dir ./      input_1.fastq 
>>> --dont_gzip  && if [ -f input_1_trimmed.fq.gz ] ; then mv
>>> input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f
>>> input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ;
>>> fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz
>>> input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv
>>> input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f
>>> input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz
>>> input_2_unpaired_2.fq ; fi
>>>
>>>
>>>
>>> In fact most of the tools do this post-upgrade - where they cannot find
>>> a file.
>>>
>>> Here is the trace from hisat2 - it fails in a similar way so we conclude
>>> that there is a common underlying fault here that is affecting the
>>> pathing of the scripts.
>>>
>>> Any ideas how we should go about finding this error?
>>>
>>> Thanks, Gerhard
>>>
>>> PS Here is the hisat2 output.
>>>
>>> #!/bin/bash
>>>
>>> # The following block can be used by the job system
>>>
>>> # to ensure this script is runnable before actually attempting
>>>
>>> # to run it.
>>>
>>> if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
>>>
>>>      exit 42
>>>
>>> fi
>>>
>>> [ "$CONDA_DEFAULT_ENV" =
>>> "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426"
>>> ] ||
>>>
>>> MAX_TRIES=3
>>>
>>> COUNT=0
>>>
>>> while [ $COUNT -lt $MAX_TRIES ]; do
>>>
>>>      . /home/.galaxy/tooldeps/_conda/bin/activate
>>> '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
>>>  > conda_activate.log 2>&1
>>>
>>>      if [ $? -eq 0 ];then
>>>
>>>          break
>>>
>>>      else
>>>
>>>          let COUNT=COUNT+1
>>>
>>>          if [ $COUNT -eq $MAX_TRIES ];then
>>>
>>>              echo "Failed to activate conda environment! Error was:"
>>>
>>>              cat conda_activate.log
>>>
>>>              exit 1
>>>
>>>          fi
>>>
>>>          sleep 10s
>>>
>>>      fi
>>>
>>> done ; [ "$CONDA_DEFAULT_ENV" =
>>> "/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426"
>>> ] ||
>>>
>>> MAX_TRIES=3
>>>
>>> COUNT=0
>>>
>>> while [ $COUNT -lt $MAX_TRIES ]; do
>>>
>>>      . /home/.galaxy/tooldeps/_conda/bin/activate
>>> '/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
>>>  > conda_activate.log 2>&1
>>>
>>>      if [ $? -eq 0 ];then
>>>
>>>          break
>>>
>>>      else
>>>
>>>          let COUNT=COUNT+1
>>>
>>>          if [ $COUNT -eq $MAX_TRIES ];then
>>>
>>>              echo "Failed to activate conda environment! Error was:"
>>>
>>>              cat conda_activate.log
>>>
>>>              exit 1
>>>
>>>          fi
>>>
>>>          sleep 10s
>>>
>>>      fi
>>>
>>> done ; hisat2 --version >
>>> /scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7484 2>&1; set -o | grep -q
>>> pipefail && set -o pipefail;   ln -s
>>> '/home/.galaxy/database/files/013/dataset_13248.dat' genome.fa &&
>>> _hisat2-build_ -p ${GALAXY_SLOTS:-1} genome.fa genome &&        ln -f -s
>>> '/home/.galaxy/database/files/013/dataset_13238.dat' input_f.fastq && 
>>> ln -f -s '/home/.galaxy/database/files/013/dataset_13243.dat'
>>> input_r.fastq &&     hisat2  -p ${GALAXY_SLOTS:-1}  -x 'genome'     -1
>>> 'input_f.fastq' -2 'input_r.fastq'                               |
>>> samtools sort - -@ ${GALAXY_SLOTS:-1} -l 6 -o
>>> '/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat'
>>>
>>> The job fails when it cannot find “hisat2-build”.
>>>
>>> Fatal error: Exit code 127 ()
>>>
>>> /home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41:
>>> hisat2-build: command not found
>>>
>>> The PATH variable should be exported with installation
>>> (/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh):
>>>
>>> PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH;
>>> export PATH
>>>
>>> HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43;
>>> export HISAT2_ROOT_DIR
>>>
>>> HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43;
>>> export HISAT_ROOT_DIR
>>>
>>> The conda environment with dependencies seems to be there:
>>>
>>> /home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin
>>>
>>>
>>>
>>>
>>> Björn Grüning <[hidden email]>;
>>> [hidden email]
>>>
>>> ------------------------------------------------------------------------
>>> *From:* Björn Grüning <[hidden email]>
>>> *Sent:* 05 July 2018 22:00:58
>>> *To:* Van Wageningen, GERHARD [[hidden email]];
>>> [hidden email]
>>> *Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
>>> environment
>>> Hi Gerhard,
>>>
>>> it seems your tool is picking up the old tool_dependency version and not
>>> the conda version of python.
>>>
>>> Have a look at
>>> https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample
>
>>
>>>
>>> <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
>>>       
>>> galaxyproject/galaxy
>>> <https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>
>>> github.com
>>> galaxy - Data intensive science for everyone.
>>>
>>>
>>>
>>> to configure the order of dependency resolution in Galaxy.
>>>
>>> Cheers,
>>> Bjoern
>>>
>>>> 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:
>>>>
>>>>
>>>> Thanks, hopefully someone has seen this before ...
>>>>
>>>>
>>>> regards, Gerhard
>>>>
>>>>
>>>>
>>>> [program:web]
>>>> command         = uwsgi --plugin python --virtualenv /home/.galaxy/.venv
>>>> --ini-paste /home/.galaxy/config/galaxy.ini
>>>> directory       = /home/.galaxy
>>>> umask           = 022
>>>> autostart       = true
>>>> autorestart     = true
>>>> startsecs       = 10
>>>> user            = galaxy
>>>> numprocs        = 1
>>>> stopsignal      = INT
>>>>
>>>> [program:handler]
>>>> command         = python ./scripts/galaxy-main -c
>>>> /home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s
>>>> directory       = /home/.galaxy
>>>> process_name    = handler%(process_num)s
>>>> numprocs        = 1
>>>> umask           = 022
>>>> autostart       = true
>>>> autorestart     = true
>>>> startsecs       = 10
>>>> user            = galaxy
>>>> environment     =
>>>> VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/"
>>>> stdout_logfile  = /home/.galaxy/handler%(process_num)s.log
>>>> redirect_stderr = true
>>>>
>>>> [group:galaxy]
>>>> programs        = handler, web
>>>>
>>>> <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 >
>>>>
>>>>
>>>> ___________________________________________________________
>>>> 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/
>>>>
>>> <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 >
>> <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 >
> <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 >

The integrity and confidentiality of this email is governed by these terms. Disclaimer
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule

___________________________________________________________
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/