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Question: Purging Datasets Problem
0
gravatar for mccoykg
3.3 years ago by
mccoykg • 80
United States
mccoykg • 80 wrote:

Hi all. I've been using the instructions here to attempt purging old datasets, but it only gives me errors. From using the command "python cleanup_datasets.py config/galaxy.ini -d 5 -1 -r", for example, I get back the following error:

Traceback (most recent call last):
  File "cleanup_datasets.py", line 13, in <module>
    from galaxy import eggs
ImportError: No module named galaxy

Does anyone know how to resolve this error or work around it? I don't want to just delete datasets in case that causes errors in identifying files, but there is very little space left on my computer, and I may need to do something like that if I can't use the cleanup scripts. Thanks much.
purging galaxy • 1.1k views
ADD COMMENT • link •
modified 3.3 years ago by Hotz, Hans-Rudolf • 1.8k • written 3.3 years ago by mccoykg • 80
1
gravatar for Hotz, Hans-Rudolf
3.3 years ago by
Hotz, Hans-Rudolf • 1.8k
Switzerland
Hotz, Hans-Rudolf • 1.8k wrote:

Hi

 

try executing the script from the <GALAXY_ROOT> directory, eg <GALAXY_ROOT>/scripts/cleanup_datasets/cleanup_datasets.py

 

Regards, Hans-Rudolf
ADD COMMENT • link written 3.3 years ago by Hotz, Hans-Rudolf • 1.8k

Just to let you know. This functionality is now also available in the admin menu for every user.

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

That'd be really convenient - do you know what header (like Manage Users, Manage Data Libraries, Manage Jobs) it would be under? I've tried looking through them but can't find where you purge datatsets.

ADD REPLY • link written 3.3 years ago by mccoykg • 80

Admin -> Users -> Pick one user and use the drop-down menu from this user -> [Delete, Recalculate Disc usage, Manage Rols and Groups]

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

I've gone there, but I don't think any of the options - delete, recalculate disc usage, or manage roles and groups - allows you to purge datasets. The delete option for example just deletes user accounts.

ADD REPLY • link written 3.3 years ago by mccoykg • 80

Sorry to pester you, but did you ever figure out where the option to purge datasets is in the admin menu? It would be really useful to know in future.

ADD REPLY • link written 3.3 years ago by mccoykg • 80
1

As I wrote above: Admin -> Users -> Pick one user and use the drop-down menu from this user -> [Delete, Recalculate Disc usage, Manage Rols and Groups]

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

Thanks! That helped, but I now get the following error:

Traceback (most recent call last):
  File "scripts/cleanup_datasets/cleanup_datasets.py", line 524, in <module>
    if __name__ == "__main__": main()
  File "scripts/cleanup_datasets/cleanup_datasets.py", line 82, in main
    ini_file = args[0]
IndexError: list index out of range

ADD REPLY • link written 3.3 years ago by mccoykg • 80

how does your full command look like now?

ADD REPLY • link written 3.3 years ago by Hotz, Hans-Rudolf • 1.8k

from the galaxy root (just galaxy for me) my command is: python scripts/cleanup_datasets/cleanup_datasets.py -d 5 -1 -r

ADD REPLY • link written 3.3 years ago by mccoykg • 80
1

try (as in your original command):

python scripts/cleanup_datasets/cleanup_datasets.py  config/galaxy.ini -d 5 -1 -r

 

 

 

ADD REPLY • link written 3.3 years ago by Hotz, Hans-Rudolf • 1.8k

That did it, thanks! I'm not sure why, but I just ran it all in order (from 1 to 5) and it managed to work like a charm.

ADD REPLY • link modified 3.3 years ago • written 3.3 years ago by mccoykg • 80
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