installation/conda problems

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installation/conda problems

Matthias Bernt
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,
[hidden email], 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
-------------------------------------------
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Re: installation/conda problems

Björn Grüning-3
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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in your mail client.  To manage your subscriptions to this
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Re: installation/conda problems

Marius van den Beek
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), 
This hasn't made it into bioblend yet (but we should do that!).

Best,
Marius

On 5 September 2017 at 17:32, Björn Grüning <[hidden email]> 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 <a href="tel:05.09.2017%2017" value="+31509201717">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:
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  http://galaxyproject.org/search/


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Re: installation/conda problems

Matthias Bernt
In reply to this post by Björn Grüning-3
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,
[hidden email], 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
-------------------------------------------
___________________________________________________________
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/