Dear list, I think I have messed up the environment for one tool (IntaRNA) -- can someone tell me what to do to get a clear environment? Here is what happened. I have started the installation (via ansible) and accidentally aborted it. Then the tool gave me the following error: ``` Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks. Fatal error: Exit code 1 (Error occurred. Please check Tool Standard Error) ``` Since uninstalling and reinstallation (via ansible) gave the same result I tried to reinstall from the Galaxy UI. Now I got (even if if the admin interface list the tool as installed): ``` Fatal error: Exit code 127 (Error occurred. Please check Tool Standard Error) /gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/000/362/tool_script.sh: line 25: IntaRNA: command not found ``` Is there a list of directories and files that I could clear to get rid of any trace of the tool and start anew? Best, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------
Hi Matthias, please have a look into your <tool-deps/_conda/env/ folder. Do you see any `__intarna...` folder? If so try to remove this one. Cheers, Bjoern On 05.09.2017 17:21, Matthias Bernt wrote:
Dear list,
I think I have messed up the environment for one tool (IntaRNA) -- can someone tell me what to do to get a clear environment? Here is what happened.
I have started the installation (via ansible) and accidentally aborted it. Then the tool gave me the following error:
``` Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks. Fatal error: Exit code 1 (Error occurred. Please check Tool Standard Error) ```
Since uninstalling and reinstallation (via ansible) gave the same result I tried to reinstall from the Galaxy UI. Now I got (even if if the admin interface list the tool as installed):
``` Fatal error: Exit code 127 (Error occurred. Please check Tool Standard Error) /gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/000/362/tool_script.sh: line 25: IntaRNA: command not found ```
Is there a list of directories and files that I could clear to get rid of any trace of the tool and start anew?
Best, Matthias
Hi Matthias, Adding to Bjoern's suggestion you can also check in the admin section under "Manage Tool Dependencies" into which path the dependency has been installed (it may be mulled-<hash>), and from there you can also uninstall the dependency. You can also trigger uninstall of the conda dependency through the API (the normal toolshed API does not uninstall conda dependencies), an example for doing this can be found here: https://github.com/galaxyproject/galaxy/blob/dev/test/integration/test_resol... . This hasn't made it into bioblend yet (but we should do that!). Best, Marius On 5 September 2017 at 17:32, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Matthias,
please have a look into your <tool-deps/_conda/env/ folder. Do you see any `__intarna...` folder? If so try to remove this one.
Cheers, Bjoern
On 05.09.2017 17:21, Matthias Bernt wrote:
Dear list,
I think I have messed up the environment for one tool (IntaRNA) -- can someone tell me what to do to get a clear environment? Here is what happened.
I have started the installation (via ansible) and accidentally aborted it. Then the tool gave me the following error:
``` Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks. Fatal error: Exit code 1 (Error occurred. Please check Tool Standard Error) ```
Since uninstalling and reinstallation (via ansible) gave the same result I tried to reinstall from the Galaxy UI. Now I got (even if if the admin interface list the tool as installed):
``` Fatal error: Exit code 127 (Error occurred. Please check Tool Standard Error) /gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/000/362/tool_script.sh: line 25: IntaRNA: command not found ```
Is there a list of directories and files that I could clear to get rid of any trace of the tool and start anew?
Best, Matthias
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Hi Bjoern and Marius, thanks for the help that did the trick. Unfortunatelly IntaRNA is still not running (apparently a dependency problem): https://github.com/bgruening/galaxytools/issues/624 Cheers, Matthias On 05.09.2017 17:32, Björn Grüning wrote:
Hi Matthias,
please have a look into your <tool-deps/_conda/env/ folder. Do you see any `__intarna...` folder? If so try to remove this one.
Cheers, Bjoern
On 05.09.2017 17:21, Matthias Bernt wrote:
Dear list,
I think I have messed up the environment for one tool (IntaRNA) -- can someone tell me what to do to get a clear environment? Here is what happened.
I have started the installation (via ansible) and accidentally aborted it. Then the tool gave me the following error:
``` Failed to activate conda environment! Error was: CondaEnvironmentError: Environment error: Cannot activate environment bash. User does not have write access for conda symlinks. Fatal error: Exit code 1 (Error occurred. Please check Tool Standard Error) ```
Since uninstalling and reinstallation (via ansible) gave the same result I tried to reinstall from the Galaxy UI. Now I got (even if if the admin interface list the tool as installed):
``` Fatal error: Exit code 127 (Error occurred. Please check Tool Standard Error) /gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/000/362/tool_script.sh: line 25: IntaRNA: command not found ```
Is there a list of directories and files that I could clear to get rid of any trace of the tool and start anew?
Best, Matthias
-- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------
participants (3)
-
Björn Grüning -
Marius van den Beek -
Matthias Bernt