Dear Nicola, thanks it worked.  cheers, Philipp -----Original message----- From: Nicola Soranzo <nsoranzo@tiscali.it> Sent: Tuesday 23rd February 2016 20:35 To: Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de>; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] cleanup 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>: 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:

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       >       >       >       > ___________________________________________________________       > 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/mailinglists/       >

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