[galaxy-dev] Re: conda not installing deps.

2019-07-29 Thread 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
 

 

Gildas


Gildas Le Corguillé - Bioinformatician/Bioanalyste

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

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


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


Station Biologique de Roscoff
Sorbonne Université / CNRS
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81



> Le 27 juil. 2019 à 11:06, Jochen Bick  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"  
> 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 +41 52 354 92 06
>>> jochen.b...@usys.ethz.ch 
>>> www.ap.ethz.ch
>>> 
>>> ___
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>>>   http://galaxyproject.org/search/
>>> 
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[galaxy-dev] Re: conda not installing deps.

2019-07-27 Thread 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

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On Jul 26, 2019, 21:07, at 21:07, "Björn Grüning"  
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 +41 52 354 92 06
>> jochen.b...@usys.ethz.ch 
>> 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/
>> 
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[galaxy-dev] Re: conda not installing deps.

2019-07-26 Thread Björn Grüning 

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 +41 52 354 92 06
jochen.b...@usys.ethz.ch 
www.ap.ethz.ch

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[galaxy-dev] Re: conda not installing deps.

2019-07-26 Thread 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 +41 52 354 92 06
> jochen.b...@usys.ethz.ch 
> 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 +41 52 354 92 06
jochen.b...@usys.ethz.ch 
www.ap.ethz.ch

___
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in your mail client.  To manage your subscriptions to this
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