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 foundIs 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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