Question: Purging Deleted Datasets
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gravatar for Erick Antezana
9.2 years ago by
Erick Antezana570 wrote:
Hi, how can I purge my deleted datasets that were imported so that I could clean a bit my disk? I saw they are under database/files/000/* thanks, Erick
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ADD COMMENTlink modified 9.2 years ago by Greg Von Kuster840 • written 9.2 years ago by Erick Antezana570
0
gravatar for Greg Von Kuster
9.2 years ago by
Greg Von Kuster840 wrote:
Hi Erick, Never do this manually as it will result in problems in your Galaxy instance. Use the ~/scripts/cleanup_datasets/cleanup_datasets.py script in the Galaxy distribution. Refer to the http://g2.trac.bx.psu.edu/wiki/PurgeHistoriesAndDatasets wiki for deatils about executing the script. The wiki is a bit outdated - we have a bitbucket ticket open ( # 99 - http://bitbucket.org/galaxy/galaxy-central/issue/99/update-the- purgehistoriesanddatasets-wiki ) to correct this. Greg Von Kuster Galaxy Development Team
ADD COMMENTlink written 9.2 years ago by Greg Von Kuster840
Hi Greg, thanks for the heads-up. the scripts work fine; however, it would be great to have such functionality from within the Admin interface (Data section?). Are there any plans to implement such request? cheers, Erick 2009/7/16 Greg Von Kuster <ghv2@psu.edu>
ADD REPLYlink written 9.2 years ago by Erick Antezana570
Hi Erick, The process we've been using on our Galaxy instances has been to set up cron to execute the shell scripts on a daily basis, something like this: # clean up datasets 0 7 * * * cd /var/opt/home/g2test/server-home/test ; sh ./scripts/cleanup_datasets/delete_userless_histories.sh ; sh ./scripts/cleanup_datasets/purge_histories.sh ; sh ./scripts/cleanup_datasets/purge_datasets.sh This works quite well, and the logs files for each of these processes can be viewed to see what occurred. We'll definitely consider adding a link to this script in the Admin view as well. Greg Von Kuster Galaxy Development Team
ADD REPLYlink written 9.2 years ago by Greg Von Kuster840
Hi Greg, are there still any plans to add a link to the clean_datasets.py script from the Admin view? Erick 2009/7/17 Greg Von Kuster <ghv2@psu.edu>:
ADD REPLYlink written 8.8 years ago by Erick Antezana570
Hello Erick, We discussed this and decided that at the current time there is no significant gain from adding this additional item to the Admin menu. The scripts have all been designed to execute via cron and can also easily be run from the command line. We don't want to configure additional threads to handle this process via the web interface. We hope this decision will not cause problems for your instance. Greg Von Kuster Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
ADD REPLYlink written 8.8 years ago by Greg Von Kuster810
Hi Greg, I have just tried out the last Galaxy sources and in particular the purging scripts. They work fine. W.r.t the decision you made, it is fine by us. Those scripts are quite well documented and they have very useful flags. cheers, Erick 2009/12/17 Greg Von Kuster <greg@bx.psu.edu>
ADD REPLYlink written 8.8 years ago by Erick Antezana570
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