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
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The wiki is a bit outdated - we have a bitbucket ticket open ( # 99 - http://bitbucket.org/galaxy/galaxy-central/issue/99/update-the-purgehistorie... ) to correct this.
Greg Von Kuster Galaxy Development Team
Erick Antezana 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
galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
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
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 The wiki is a bit outdated - we have a bitbucket ticket open ( # 99 - http://bitbucket.org/galaxy/galaxy-central/issue/99/update-the-purgehistorie...) to correct this.
Greg Von Kuster Galaxy Development Team
Erick Antezana 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
galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
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
Erick Antezana wrote:
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 mailto:ghv2@psu.edu>
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 Erick Antezana 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 ------------------------------------------------------------------------ _______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu <mailto:galaxy-user@bx.psu.edu> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
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:
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
Erick Antezana wrote:
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 mailto:ghv2@psu.edu>
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-purgehistorie... ) to correct this.
Greg Von Kuster Galaxy Development Team
Erick Antezana 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
------------------------------------------------------------------------
_______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu mailto:galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
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
On Dec 16, 2009, at 4:35 AM, Erick Antezana wrote:
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:
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
Erick Antezana wrote:
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 mailto:ghv2@psu.edu>
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
Erick Antezana 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
_______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu <mailto:galaxy-user@bx.psu.edu> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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
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
On Dec 16, 2009, at 4:35 AM, Erick Antezana wrote:
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:
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
Erick Antezana wrote:
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 <mailto:ghv2@psu.edughv2@psu.edu
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-purgehistorie... ) to correct this.
Greg Von Kuster Galaxy Development Team
Erick Antezana 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
_______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu <mailto:galaxy-user@bx.psu.edu<galaxy-user@bx.psu.edu>http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-userGreg Von Kuster Galaxy Development Team greg@bx.psu.edu
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