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.bick@usys.ethz.ch mailto:jochen.bick@usys.ethz.ch www.ap.ethz.ch
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.bick@usys.ethz.ch mailto:jochen.bick@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
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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.bick@usys.ethz.ch mailto:jochen.bick@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
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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" bjoern.gruening@gmail.com 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.bick@usys.ethz.ch mailto:jochen.bick@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
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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/ga... 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: +33 2 98 29 23 81 ----------------------------------------------------------------------------------------------------------------------------
Le 27 juil. 2019 à 11:06, Jochen Bick jochen.bick@usys.ethz.ch 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" bjoern.gruening@gmail.com 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.bick@usys.ethz.ch mailto:jochen.bick@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/
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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