conda not installing deps.

[Jochen Bick]

Hi

we have a new galaxy 19.01 instance and conda is somehow not running
correctly:

galaxy.yml

  #dependency_resolvers_config_file: config/dependency_resolvers_conf.xml
  conda_prefix: /opt/galaxy/tools/_conda
  #conda_exec: null
  #conda_debug: false
  #conda_ensure_channels: 'iuc,conda-forge,bioconda,defaults'
  #conda_use_local: false
  conda_auto_install: true
  conda_auto_init: true
  conda_copy_dependencies: true

  job_working_directory: /opt/galaxy/daten/jobs_directory

any ideas?

Thanks Jochen


       

--  
ETH Zurich
*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315 Lindau, Switzerland

Phone [phone]
[hidden email] <mailto:[hidden email]>
www.ap.ethz.ch

___________________________________________________________
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:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

[Jochen Bick]

are there any special setting needed for the _conda folder 755 ist ok?

On 25.07.19 15:45, Jochen Bick wrote:

> Hi
>
> we have a new galaxy 19.01 instance and conda is somehow not running
> correctly:
>
> galaxy.yml
>
>   #dependency_resolvers_config_file: config/dependency_resolvers_conf.xml
>   conda_prefix: /opt/galaxy/tools/_conda
>   #conda_exec: null
>   #conda_debug: false
>   #conda_ensure_channels: 'iuc,conda-forge,bioconda,defaults'
>   #conda_use_local: false
>   conda_auto_install: true
>   conda_auto_init: true
>   conda_copy_dependencies: true
>
>   job_working_directory: /opt/galaxy/daten/jobs_directory
>
> any ideas?
>
> Thanks Jochen
>
>
>        
>
> --  
> ETH Zurich
> *Jochen Bick*
> Animal Physiology
> Institute of Agricultural Sciences
> Postal address: Universitätstrasse 2 / LFW B 58.1
> 8092 Zurich, Switzerland
> Office: Eschikon 27
> 8315 Lindau, Switzerland
>
> Phone [phone]
> [hidden email] <mailto:[hidden email]>
> www.ap.ethz.ch
>
> ___________________________________________________________
> 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:
>   %(web_page_url)s
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/

--
ETH Zurich
*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315 Lindau, Switzerland

Phone [phone]
[hidden email] <mailto:[hidden email]>
www.ap.ethz.ch

___________________________________________________________
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:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

[Björn Grüning-3]

Hi Jochen,

what is not working? Do you have any error message.

Ciao,
Bjoern

Am 25.07.19 um 15:45 schrieb Jochen Bick:

> Hi
>
> we have a new galaxy 19.01 instance and conda is somehow not running
> correctly:
>
> galaxy.yml
>
>    #dependency_resolvers_config_file: config/dependency_resolvers_conf.xml
>    conda_prefix: /opt/galaxy/tools/_conda
>    #conda_exec: null
>    #conda_debug: false
>    #conda_ensure_channels: 'iuc,conda-forge,bioconda,defaults'
>    #conda_use_local: false
>    conda_auto_install: true
>    conda_auto_init: true
>    conda_copy_dependencies: true
>
>    job_working_directory: /opt/galaxy/daten/jobs_directory
>
> any ideas?
>
> Thanks Jochen
>
>
>        
>
> --
> ETH Zurich
> *Jochen Bick*
> Animal Physiology
> Institute of Agricultural Sciences
> Postal address: Universitätstrasse 2 / LFW B 58.1
> 8092 Zurich, Switzerland
> Office: Eschikon 27
> 8315 Lindau, Switzerland
>
> Phone [phone]
> [hidden email] <mailto:[hidden email]>
> www.ap.ethz.ch
>
> ___________________________________________________________
> 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:
>    %(web_page_url)s
>
> 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:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

[Jochen Bick]

Hej Björn,

We have activated all conda parameters in the yml. But when you install a tool the deps are not installed. So every tool is installed with no deps.

Jochen

⁣Get BlueMail for Android ​

On Jul 26, 2019, 21:07, at 21:07, "Björn Grüning" <[hidden email]> wrote:

>Hi Jochen,
>
>what is not working? Do you have any error message.
>
>Ciao,
>Bjoern
>
>Am 25.07.19 um 15:45 schrieb Jochen Bick:
>> Hi
>>
>> we have a new galaxy 19.01 instance and conda is somehow not running
>> correctly:
>>
>> galaxy.yml
>>
>>    #dependency_resolvers_config_file:
>config/dependency_resolvers_conf.xml
>>    conda_prefix: /opt/galaxy/tools/_conda
>>    #conda_exec: null
>>    #conda_debug: false
>>    #conda_ensure_channels: 'iuc,conda-forge,bioconda,defaults'
>>    #conda_use_local: false
>>    conda_auto_install: true
>>    conda_auto_init: true
>>    conda_copy_dependencies: true
>>
>>    job_working_directory: /opt/galaxy/daten/jobs_directory
>>
>> any ideas?
>>
>> Thanks Jochen
>>
>>
>>        
>>
>> --
>> ETH Zurich
>> *Jochen Bick*
>> Animal Physiology
>> Institute of Agricultural Sciences
>> Postal address: Universitätstrasse 2 / LFW B 58.1
>> 8092 Zurich, Switzerland
>> Office: Eschikon 27
>> 8315 Lindau, Switzerland
>>
>> Phone [phone]
>> [hidden email] <mailto:[hidden email]>
>> www.ap.ethz.ch
>>
>> ___________________________________________________________
>> 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:
>>    %(web_page_url)s
>>
>> 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:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

[Gildas Le Corguillé]

Hi Jochen,

Did you try to install the deps with the dedicated "Manage dependencies" and check the log ?
Is Conda installed in /opt/galaxy/tools/_conda/bin/conda ?

BTW, are you sure you need to enable this option? https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/galaxy.yml.sample#L265-L271 <https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/galaxy.yml.sample#L265-L271>

Gildas

----------------------------------------------------------------------------------------------------------------------------
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science): http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Co-leader of the IFB Core Cluster: https://www.france-bioinformatique.fr/en/cluster <https://www.france-bioinformatique.fr/fr/cluster>

Member of the Workflow4Metabolomics project: http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff
Sorbonne Université / CNRS
Place Georges Teissier 29680 Roscoff FRANCE
tel: [phone]
----------------------------------------------------------------------------------------------------------------------------

> Le 27 juil. 2019 à 11:06, Jochen Bick <[hidden email]> a écrit :
>
> Hej Björn,
>
> We have activated all conda parameters in the yml. But when you install a tool the deps are not installed. So every tool is installed with no deps.
>
> Jochen
>
> ⁣Get BlueMail for Android ​
>
> On Jul 26, 2019, 21:07, at 21:07, "Björn Grüning" <[hidden email]> wrote:
>> Hi Jochen,
>>
>> what is not working? Do you have any error message.
>>
>> Ciao,
>> Bjoern
>>
>> Am 25.07.19 um 15:45 schrieb Jochen Bick:
>>> Hi
>>>
>>> we have a new galaxy 19.01 instance and conda is somehow not running
>>> correctly:
>>>
>>> galaxy.yml
>>>
>>>   #dependency_resolvers_config_file:
>> config/dependency_resolvers_conf.xml
>>>   conda_prefix: /opt/galaxy/tools/_conda
>>>   #conda_exec: null
>>>   #conda_debug: false
>>>   #conda_ensure_channels: 'iuc,conda-forge,bioconda,defaults'
>>>   #conda_use_local: false
>>>   conda_auto_install: true
>>>   conda_auto_init: true
>>>   conda_copy_dependencies: true
>>>
>>>   job_working_directory: /opt/galaxy/daten/jobs_directory
>>>
>>> any ideas?
>>>
>>> Thanks Jochen
>>>
>>>
>>>
>>>
>>> --
>>> ETH Zurich
>>> *Jochen Bick*
>>> Animal Physiology
>>> Institute of Agricultural Sciences
>>> Postal address: Universitätstrasse 2 / LFW B 58.1
>>> 8092 Zurich, Switzerland
>>> Office: Eschikon 27
>>> 8315 Lindau, Switzerland
>>>
>>> Phone [phone]
>>> [hidden email] <mailto:[hidden email]>
>>> www.ap.ethz.ch
>>>
>>> ___________________________________________________________
>>> 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:
>>>   %(web_page_url)s
>>>
>>> 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:
>  %(web_page_url)s
>
> 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:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/