Dataset Cleanup

classic Classic list List threaded Threaded
4 messages Options
| Threaded
Open this post in threaded view
|

Dataset Cleanup

McCully, Dwayne (NIH/NIAMS) [C]

Hello Everyone,

 

I have datasets that go back over a year in the files/000 directory but running the following script does not delete the datasets.

Also, my account says I have 59 GB used and can’t figure out where it’s getting that number.  I have almost everything deleted

in my Galaxy account.

 

galaxy_clean.sh

#!/bin/sh -x

 

/home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_userless_histories.sh

/home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_histories.sh

/home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_libraries.sh

/home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_folders.sh

/home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_datasets.sh

/home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_datasets.sh

Exit

 

 

Any information on this issue would be appreciated.

 

Dwayne


___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Dataset Cleanup

Björn Grüning-3
Hi,

this script only deletes files that are marked as deleted. So it might
be that users have old histories and this data will not be removed.

For you account and the used-space. Please go to your admin section, to
users, your user-name and there should be an option to recalculate the
disc-usage for your user.

Hope this helps,
Bjoern

Am 03.01.2017 um 16:41 schrieb McCully, Dwayne (NIH/NIAMS) [C]:

> Hello Everyone,
>
>  
>
> I have datasets that go back over a year in the files/000 directory but
> running the following script does not delete the datasets.
>
> Also, my account says I have 59 GB used and can’t figure out where it’s
> getting that number.  I have almost everything deleted
>
> in my Galaxy account.
>
>  
>
> galaxy_clean.sh
>
> #!/bin/sh -x
>
>  
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_userless_histories.sh
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_histories.sh
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_libraries.sh
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_folders.sh
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_datasets.sh
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_datasets.sh
>
> Exit
>
>  
>
>  
>
> Any information on this issue would be appreciated.
>
>  
>
> Dwayne
>
>
>
> ___________________________________________________________
> 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/
>
___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Dataset Cleanup

McCully, Dwayne (NIH/NIAMS) [C]
Strange since I've deleted almost everything from my Galaxy account and it still says 59 GB and
another user is having the same problem.   Is there a way to tie the dataset or history to the user?
I can then ask them to delete them.

Dwayne

-----Original Message-----
From: Björn Grüning [mailto:[hidden email]]
Sent: Thursday, January 05, 2017 9:43 AM
To: McCully, Dwayne (NIH/NIAMS) [C] <[hidden email]>; [hidden email]
Subject: Re: [galaxy-dev] Dataset Cleanup

Hi,

this script only deletes files that are marked as deleted. So it might be that users have old histories and this data will not be removed.

For you account and the used-space. Please go to your admin section, to users, your user-name and there should be an option to recalculate the disc-usage for your user.

Hope this helps,
Bjoern

Am 03.01.2017 um 16:41 schrieb McCully, Dwayne (NIH/NIAMS) [C]:

> Hello Everyone,
>
>  
>
> I have datasets that go back over a year in the files/000 directory
> but running the following script does not delete the datasets.
>
> Also, my account says I have 59 GB used and can’t figure out where
> it’s getting that number.  I have almost everything deleted
>
> in my Galaxy account.
>
>  
>
> galaxy_clean.sh
>
> #!/bin/sh -x
>
>  
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_userless_hist
> ories.sh
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_histories.sh
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_libraries.sh
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_folders.sh
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_datasets.sh
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_datasets.sh
>
> Exit
>
>  
>
>  
>
> Any information on this issue would be appreciated.
>
>  
>
> Dwayne
>
>
>
> ___________________________________________________________
> 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/
>
___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Dataset Cleanup

Dannon Baker-2
The quota usage can occasionally get out of sync with reality.  If you're an admin user, go to <instance>/admin/users, select a user, and you should be able to recalculate the quota to verify it is correct.  There's also a script distributed with Galaxy (<gxy>/scripts/set_user_disk_usage.py) that allows you to recalculate across all users.  Let me know if this wasn't your issue and I can think of other possible causes.

-Dannon

On Thu, Jan 5, 2017 at 5:17 PM, McCully, Dwayne (NIH/NIAMS) [C] <[hidden email]> wrote:
Strange since I've deleted almost everything from my Galaxy account and it still says 59 GB and
another user is having the same problem.   Is there a way to tie the dataset or history to the user?
I can then ask them to delete them.

Dwayne

-----Original Message-----
From: Björn Grüning [mailto:[hidden email]]
Sent: Thursday, January 05, 2017 9:43 AM
To: McCully, Dwayne (NIH/NIAMS) [C] <[hidden email]>; [hidden email]
Subject: Re: [galaxy-dev] Dataset Cleanup

Hi,

this script only deletes files that are marked as deleted. So it might be that users have old histories and this data will not be removed.

For you account and the used-space. Please go to your admin section, to users, your user-name and there should be an option to recalculate the disc-usage for your user.

Hope this helps,
Bjoern

Am 03.01.2017 um 16:41 schrieb McCully, Dwayne (NIH/NIAMS) [C]:
> Hello Everyone,
>
>
>
> I have datasets that go back over a year in the files/000 directory
> but running the following script does not delete the datasets.
>
> Also, my account says I have 59 GB used and can’t figure out where
> it’s getting that number.  I have almost everything deleted
>
> in my Galaxy account.
>
>
>
> galaxy_clean.sh
>
> #!/bin/sh -x
>
>
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_userless_hist
> ories.sh
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_histories.sh
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_libraries.sh
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_folders.sh
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_datasets.sh
>
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_datasets.sh
>
> Exit
>
>
>
>
>
> Any information on this issue would be appreciated.
>
>
>
> Dwayne
>
>
>
> ___________________________________________________________
> 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/
>
___________________________________________________________
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/


___________________________________________________________
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/