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_resolvers.py#L109 . 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.gruen...@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 > > > > > > > > > > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ >
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