[galaxy-dev] September Galaxy Newsletter

[Dave Clements]

Hello all,

The September 2017 Galaxy News
 is out and there are
new publications (122 of them)
, events
, open
positions  in
France and the US, ToolShed contributions
,
and new releases of nebulizer
 and
CloudBridge
.
August also saw the initial release of Takeru Galaxy
, a fully
configured (hardware and software) Galaxy server; and Galaskio
, an easy to
use GUI for running Galaxy workflows.

See the full newsletter .
Thanks for using Galaxy,

The Galaxy Team

-- 
https://galaxyproject.org/
https://usegalaxy.org/
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Re: [galaxy-dev] installation/conda problems

[Matthias Bernt]

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 
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.be...@ufz.de, www.ufz.de

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Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
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