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

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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

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