Re: [galaxy-dev] cleanup

23 Feb 2016

      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:
1. 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
2. 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>
     *Sent:* Monday 22nd February 2016 17:09
     *To:* Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de>;
     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>
     >
     > http://www.ibc.uni-stuttgart.de/
     >
     > http://www.ibc.uni-stuttgart.de/mitarbeiter/Rathert/?__locale=en
     >
     >
     >
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