New subject: cleanup

23 Feb 2016

      Hi Philipp,
please alway reply to the mailing list.
I'm not using Docker, but if Galaxy is in the /galaxy-central/ directory 
and its version is 16.01, then:
$ cd /galaxy-central/
$ . .venv/bin/activate
$ python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini 
-d -30 -1
$ deactivate
The command ". .venv/bin/activate" will activate the virtualenv 
installed in /galaxy-central/.venv/ , "deactivate" will deactivate it.
Cheers,
Nicola
On 23/02/16 19:14, Rathert, Philipp, Dr. wrote:
...
Hi Nicola,
Could you be a bit more specific?
I guess i activate this in the specific container but how exactly?
Thanks a lot for your help.
Cheers,
Philipp
---Philipp on the road---
Am 23.02.2016 um 16:20 schrieb Nicola Soranzo <nsoranzo@tiscali.it 
mailto:nsoranzo@tiscali.it>:
...
Hi Philipp,
if you are using Galaxy release 16.01, you should load the virtualenv
before running the cleanup script, e.g.:
$ cd GALAXY_HOME
$ . .venv/bin/activate
$ python scripts/cleanup_datasets/cleanup_datasets.py ...
Cheers,
Nicola
On 23/02/16 15:07, Hans-Rudolf Hotz wrote:
...
Hi Philipp
point 1 : that's as expected - good.
point 2 : looks like a docker specific issue? Maybe Bjoern can jump in?
Hans-Rudolf
On 02/23/2016 12:17 PM, Rathert, Philipp, Dr. wrote:
...
Dear Hans-Rudolf,
thanks a lot for your help.
I did as you suggested:

when I go into the scripts folder I get the error message you

guessed:
root@galaxy:/galaxy-central/scripts# python
cleanup_datasets/cleanup_datasets.py
/export/galaxy-central/config/galaxy.ini -d -30 -1
Traceback (most recent call last):
    File "cleanup_datasets/cleanup_datasets.py", line 21, in <module>
      import galaxy.config
ImportError: No module named galaxy.config

from the root directory I recieve the following error message:

root@galaxy:/galaxy-central# python
scripts/cleanup_datasets/cleanup_datasets.py
/export/galaxy-central/config/galaxy.ini -d -60 -1
Traceback (most recent call last):
    File "scripts/cleanup_datasets/cleanup_datasets.py", line 21, in
<module>
      import galaxy.config
    File "/galaxy-central/lib/galaxy/config.py", line 21, in <module>
      from galaxy.util.dbkeys import GenomeBuilds
    File "/galaxy-central/lib/galaxy/util/dbkeys.py", line 7, in
<module>
      from galaxy.util.object_wrapper import sanitize_lists_to_string
    File "/galaxy-central/lib/galaxy/util/object_wrapper.py", line
45, in
<module>
      from six.moves import UserDict
ImportError: cannot import name UserDict
Any idea what this means? I thought this should be automatically
installed with python...
Cheers,
Philipp
 -----Original message-----
 *From:* Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>>
 *Sent:* Monday 22nd February 2016 17:09
 *To:* Rathert, Philipp, Dr. 

<philipp.rathert@ibc.uni-stuttgart.de 
mailto:philipp.rathert@ibc.uni-stuttgart.de>;
...
...
galaxy-dev@lists.galaxyproject.org
mailto:galaxy-dev@lists.galaxyproject.org
...
...
 *Subject:* Re: [galaxy-dev] cleanup

 Hi Philipp

 > Since the new galaxy version, I am unable to perform a cleanup

anymore.
     >
     >  From the galaxy root directory I want to start the script
     > cleanup_datasets.py with the following line:
     >
     > $ python cleanup_datasets.py
/export/galaxy-central/config/galaxy.ini -d
     > -60 -1
     >
     > I get the error message:
     >
     > Can’t open file ‘cleanup_datasets.py’: no such file or
directory.
...
...
 Have you tried:

 $ python scripts/cleanup_datasets/cleanup_datasets.py
 /export/galaxy-central/config/galaxy.ini -d -60 -1

 > But when I go into the folder in which the script is located

it doesn’t
     > work as well.
 what is the error this time? Is it "ImportError: No module named

galaxy"?
 Regards, Hans-Rudolf

 > For your information: we are running the latest

docker-galaxy-stable
     > version.
     >
     > I hope somebody has an idea.
     >
     > Cheers,
     >
     > Philipp
     >
     > ----------------------------------------------
     >
     > Philipp Rathert, PhD
     >
     > Institute of Biochemistry
     >
     > University Stuttgart
     >
     > Pfaffenwaldring 55
     >
     > D-70569 Stuttgart
     >
     > Germany
     >
     > Tel: +49 711 685 64388
     >
     > Fax: +49 711 685 64392
     >
     > philipp.rathert@ibc.uni-stuttgart.de
mailto:philipp.rathert@ibc.uni-stuttgart.de
...
...
 > <mailto:philipp.rathert@ibc.uni-stuttgart.de>
 >
 > http://www.ibc.uni-stuttgart.de/
 >
 > 

http://www.ibc.uni-stuttgart.de/mitarbeiter/Rathert/?__locale=en
...
...
 >
 >
 >
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