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 [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/ |
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 > [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 +41 52 354 92 06 [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/ |
In reply to this post by Jochen Bick
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 > [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/ |
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 +41 52 354 92 06 >> [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/ |
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: +33 2 98 29 23 81 ---------------------------------------------------------------------------------------------------------------------------- > 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 +41 52 354 92 06 >>> [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/ |
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