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 -------------------------------------------