how to delete datasets or save space on local galaxy
Dear there, May I ask a question which might be really simple? How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it. [cid:d28891d2-9d20-4688-8e3e-3bf75caa662e] Thank you so much! Best, Xiaofei
Hi Xiaofei, The (x) simply flags a dataset for deletion, it does not remove it from disk. This happens when the instance maintainers run cleanup scripts. If your instance is so configured, you can use the "Purge Deleted Datasets" option to immediately remove datasets from disk. -Dannon On Fri, Apr 11, 2014 at 5:33 PM, Wang, Xiaofei <xfwang@ku.edu> wrote:
Dear there,
May I ask a question which might be really simple?
How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it.
Thank you so much!
Best,
Xiaofei
___________________________________________________________ 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: http://lists.bx.psu.edu/
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Hi Dannon, Could you tell me how to edit the configure file? What I see from here https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20... is how to use the command line, correct? Thanks a lot! Best, Xiaofei ________________________________ From: Dannon Baker [dannon.baker@gmail.com] Sent: Friday, April 11, 2014 4:42 PM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] how to delete datasets or save space on local galaxy Hi Xiaofei, The (x) simply flags a dataset for deletion, it does not remove it from disk. This happens when the instance maintainers run cleanup scripts. If your instance is so configured, you can use the "Purge Deleted Datasets" option to immediately remove datasets from disk. -Dannon On Fri, Apr 11, 2014 at 5:33 PM, Wang, Xiaofei <xfwang@ku.edu<mailto:xfwang@ku.edu>> wrote: Dear there, May I ask a question which might be really simple? How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it. [cid:d28891d2-9d20-4688-8e3e-3bf75caa662e] Thank you so much! Best, Xiaofei ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hey, sure. The option you're looking for is "allow_user_dataset_purge", around line 650 or so. Good luck! -Dannon On Fri, Apr 11, 2014 at 5:53 PM, Wang, Xiaofei <xfwang@ku.edu> wrote:
Hi Dannon,
Could you tell me how to edit the configure file?
What I see from here https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20... is how to use the command line, correct?
Thanks a lot!
Best,
Xiaofei ------------------------------ *From:* Dannon Baker [dannon.baker@gmail.com] *Sent:* Friday, April 11, 2014 4:42 PM *To:* Wang, Xiaofei *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] how to delete datasets or save space on local galaxy
Hi Xiaofei,
The (x) simply flags a dataset for deletion, it does not remove it from disk. This happens when the instance maintainers run cleanup scripts. If your instance is so configured, you can use the "Purge Deleted Datasets" option to immediately remove datasets from disk.
-Dannon
On Fri, Apr 11, 2014 at 5:33 PM, Wang, Xiaofei <xfwang@ku.edu> wrote:
Dear there,
May I ask a question which might be really simple?
How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it.
Thank you so much!
Best,
Xiaofei
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
I replied too soon. To answer your second question, yes, that's how to use the cleanup scripts from the command line. Enabling the option from my previous email will allow users to *immediately* purge datasets without waiting on those cleanup scripts. -Dannon On Fri, Apr 11, 2014 at 5:55 PM, Dannon Baker <dannon.baker@gmail.com>wrote:
Hey, sure. The option you're looking for is "allow_user_dataset_purge", around line 650 or so.
Good luck!
-Dannon
On Fri, Apr 11, 2014 at 5:53 PM, Wang, Xiaofei <xfwang@ku.edu> wrote:
Hi Dannon,
Could you tell me how to edit the configure file?
What I see from here https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20... is how to use the command line, correct?
Thanks a lot!
Best,
Xiaofei ------------------------------ *From:* Dannon Baker [dannon.baker@gmail.com] *Sent:* Friday, April 11, 2014 4:42 PM *To:* Wang, Xiaofei *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] how to delete datasets or save space on local galaxy
Hi Xiaofei,
The (x) simply flags a dataset for deletion, it does not remove it from disk. This happens when the instance maintainers run cleanup scripts. If your instance is so configured, you can use the "Purge Deleted Datasets" option to immediately remove datasets from disk.
-Dannon
On Fri, Apr 11, 2014 at 5:33 PM, Wang, Xiaofei <xfwang@ku.edu> wrote:
Dear there,
May I ask a question which might be really simple?
How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it.
Thank you so much!
Best,
Xiaofei
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Yes, it works. But, I am still a little bit confuse about the size on the top right corner. Why does not it change after purging datasets? ________________________________ From: Dannon Baker [dannon.baker@gmail.com] Sent: Friday, April 11, 2014 4:57 PM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] how to delete datasets or save space on local galaxy I replied too soon. To answer your second question, yes, that's how to use the cleanup scripts from the command line. Enabling the option from my previous email will allow users to *immediately* purge datasets without waiting on those cleanup scripts. -Dannon On Fri, Apr 11, 2014 at 5:55 PM, Dannon Baker <dannon.baker@gmail.com<mailto:dannon.baker@gmail.com>> wrote: Hey, sure. The option you're looking for is "allow_user_dataset_purge", around line 650 or so. Good luck! -Dannon On Fri, Apr 11, 2014 at 5:53 PM, Wang, Xiaofei <xfwang@ku.edu<mailto:xfwang@ku.edu>> wrote: Hi Dannon, Could you tell me how to edit the configure file? What I see from here https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20... is how to use the command line, correct? Thanks a lot! Best, Xiaofei ________________________________ From: Dannon Baker [dannon.baker@gmail.com<mailto:dannon.baker@gmail.com>] Sent: Friday, April 11, 2014 4:42 PM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] how to delete datasets or save space on local galaxy Hi Xiaofei, The (x) simply flags a dataset for deletion, it does not remove it from disk. This happens when the instance maintainers run cleanup scripts. If your instance is so configured, you can use the "Purge Deleted Datasets" option to immediately remove datasets from disk. -Dannon On Fri, Apr 11, 2014 at 5:33 PM, Wang, Xiaofei <xfwang@ku.edu<mailto:xfwang@ku.edu>> wrote: Dear there, May I ask a question which might be really simple? How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it. [cid:d28891d2-9d20-4688-8e3e-3bf75caa662e] Thank you so much! Best, Xiaofei ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hello, That's a good question! Does the size in the top right change when the page is reloaded? Are these datasets copied from another history? How are you purging the datasets? As Dannon mentioned, if you click the 'X' button on the dataset it will 'mark' the dataset as deleted. To permanently deleted the datasets (or 'purge' them), you can: 1. Mark them deleted using the 'X' button on the dataset, 2. Then from the history options menu (the button that looks like a gear at the top of the history), select 'Include deleted datasets'. This will make the dataset you marked as deleted visible in the history again. 3. In the deleted dataset you'll see a yellow box explaining that the history has been deleted and showing two links: one for undeleting the dataset (which will undo the deletion of the dataset) and one for immediately removing it from disk - this link will purge the dataset. Click the second link. You can hide the deleted datasets again by clicking: history options menu -> 'Include deleted datasets' again. If you do the above, does the size in the top right change or still remain the same? Let me know if you need more info, Carl On Fri, Apr 11, 2014 at 6:25 PM, Wang, Xiaofei <xfwang@ku.edu> wrote:
Yes, it works. But, I am still a little bit confuse about the size on the top right corner. Why does not it change after purging datasets? ------------------------------ *From:* Dannon Baker [dannon.baker@gmail.com] *Sent:* Friday, April 11, 2014 4:57 PM
*To:* Wang, Xiaofei *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] how to delete datasets or save space on local galaxy
I replied too soon. To answer your second question, yes, that's how to use the cleanup scripts from the command line. Enabling the option from my previous email will allow users to *immediately* purge datasets without waiting on those cleanup scripts.
-Dannon
On Fri, Apr 11, 2014 at 5:55 PM, Dannon Baker <dannon.baker@gmail.com>wrote:
Hey, sure. The option you're looking for is "allow_user_dataset_purge", around line 650 or so.
Good luck!
-Dannon
On Fri, Apr 11, 2014 at 5:53 PM, Wang, Xiaofei <xfwang@ku.edu> wrote:
Hi Dannon,
Could you tell me how to edit the configure file?
What I see from here https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20... is how to use the command line, correct?
Thanks a lot!
Best,
Xiaofei ------------------------------ *From:* Dannon Baker [dannon.baker@gmail.com] *Sent:* Friday, April 11, 2014 4:42 PM *To:* Wang, Xiaofei *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] how to delete datasets or save space on local galaxy
Hi Xiaofei,
The (x) simply flags a dataset for deletion, it does not remove it from disk. This happens when the instance maintainers run cleanup scripts. If your instance is so configured, you can use the "Purge Deleted Datasets" option to immediately remove datasets from disk.
-Dannon
On Fri, Apr 11, 2014 at 5:33 PM, Wang, Xiaofei <xfwang@ku.edu> wrote:
Dear there,
May I ask a question which might be really simple?
How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it.
Thank you so much!
Best,
Xiaofei
___________________________________________________________ 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: http://lists.bx.psu.edu/
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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Carl, The size is changed when the page is reloaded. Here is how I purge the data: 1. Mark them deleted using the "X" button on the dataset 2. From the history options menu, select 'Purge Deleted Datasets' I think this will purge the deleted datasets too (correct?) because in the yellow box it shows that "This dataset has been deleted and removed from disk". But I am not sure if there is any difference with the 3-steps that you advised. I think the difference might be that it can purge the dataset one by one in your advice, is it? Thanks Xiaofei From: Carl Eberhard [carlfeberhard@gmail.com] Sent: Monday, April 14, 2014 8:47 AM To: Wang, Xiaofei Cc: Dannon Baker; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] how to delete datasets or save space on local galaxy Hello, That's a good question! Does the size in the top right change when the page is reloaded? Are these datasets copied from another history? How are you purging the datasets? As Dannon mentioned, if you click the 'X' button on the dataset it will 'mark' the dataset as deleted. To permanently deleted the datasets (or 'purge' them), you can: 1. Mark them deleted using the 'X' button on the dataset, 2. Then from the history options menu (the button that looks like a gear at the top of the history), select 'Include deleted datasets'. This will make the dataset you marked as deleted visible in the history again. 3. In the deleted dataset you'll see a yellow box explaining that the history has been deleted and showing two links: one for undeleting the dataset (which will undo the deletion of the dataset) and one for immediately removing it from disk - this link will purge the dataset. Click the second link. You can hide the deleted datasets again by clicking: history options menu -> 'Include deleted datasets' again. If you do the above, does the size in the top right change or still remain the same? Let me know if you need more info, Carl On Fri, Apr 11, 2014 at 6:25 PM, Wang, Xiaofei <xfwang@ku.edu<mailto:xfwang@ku.edu>> wrote: Yes, it works. But, I am still a little bit confuse about the size on the top right corner. Why does not it change after purging datasets? ________________________________ From: Dannon Baker [dannon.baker@gmail.com<mailto:dannon.baker@gmail.com>] Sent: Friday, April 11, 2014 4:57 PM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] how to delete datasets or save space on local galaxy I replied too soon. To answer your second question, yes, that's how to use the cleanup scripts from the command line. Enabling the option from my previous email will allow users to *immediately* purge datasets without waiting on those cleanup scripts. -Dannon On Fri, Apr 11, 2014 at 5:55 PM, Dannon Baker <dannon.baker@gmail.com<mailto:dannon.baker@gmail.com>> wrote: Hey, sure. The option you're looking for is "allow_user_dataset_purge", around line 650 or so. Good luck! -Dannon On Fri, Apr 11, 2014 at 5:53 PM, Wang, Xiaofei <xfwang@ku.edu<mailto:xfwang@ku.edu>> wrote: Hi Dannon, Could you tell me how to edit the configure file? What I see from here https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20... is how to use the command line, correct? Thanks a lot! Best, Xiaofei ________________________________ From: Dannon Baker [dannon.baker@gmail.com<mailto:dannon.baker@gmail.com>] Sent: Friday, April 11, 2014 4:42 PM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] how to delete datasets or save space on local galaxy Hi Xiaofei, The (x) simply flags a dataset for deletion, it does not remove it from disk. This happens when the instance maintainers run cleanup scripts. If your instance is so configured, you can use the "Purge Deleted Datasets" option to immediately remove datasets from disk. -Dannon On Fri, Apr 11, 2014 at 5:33 PM, Wang, Xiaofei <xfwang@ku.edu<mailto:xfwang@ku.edu>> wrote: Dear there, May I ask a question which might be really simple? How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it. [cid:d28891d2-9d20-4688-8e3e-3bf75caa662e] Thank you so much! Best, Xiaofei ___________________________________________________________ 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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
You're absolutely right. That is a bug with that particular method of purging. I've created a card for it here: https://trello.com/c/bvOL9IBb. Thanks very much for finding that. On Mon, Apr 14, 2014 at 11:31 AM, Wang, Xiaofei <xfwang@ku.edu> wrote:
Hi Carl,
The size is changed when the page is reloaded. Here is how I purge the data:
1. Mark them deleted using the "X" button on the dataset 2. From the history options menu, select 'Purge Deleted Datasets'
I think this will purge the deleted datasets too (correct?) because in the yellow box it shows that "This dataset has been deleted and removed from disk". But I am not sure if there is any difference with the 3-steps that you advised. I think the difference might be that it can purge the dataset one by one in your advice, is it?
Thanks
Xiaofei
*From:* Carl Eberhard [carlfeberhard@gmail.com] *Sent:* Monday, April 14, 2014 8:47 AM *To:* Wang, Xiaofei *Cc:* Dannon Baker; galaxy-dev@lists.bx.psu.edu
*Subject:* Re: [galaxy-dev] how to delete datasets or save space on local galaxy
Hello,
That's a good question! Does the size in the top right change when the page is reloaded? Are these datasets copied from another history?
How are you purging the datasets? As Dannon mentioned, if you click the 'X' button on the dataset it will 'mark' the dataset as deleted. To permanently deleted the datasets (or 'purge' them), you can:
1. Mark them deleted using the 'X' button on the dataset, 2. Then from the history options menu (the button that looks like a gear at the top of the history), select 'Include deleted datasets'. This will make the dataset you marked as deleted visible in the history again. 3. In the deleted dataset you'll see a yellow box explaining that the history has been deleted and showing two links: one for undeleting the dataset (which will undo the deletion of the dataset) and one for immediately removing it from disk - this link will purge the dataset. Click the second link.
You can hide the deleted datasets again by clicking: history options menu -> 'Include deleted datasets' again.
If you do the above, does the size in the top right change or still remain the same?
Let me know if you need more info, Carl
On Fri, Apr 11, 2014 at 6:25 PM, Wang, Xiaofei <xfwang@ku.edu> wrote:
Yes, it works. But, I am still a little bit confuse about the size on the top right corner. Why does not it change after purging datasets? ------------------------------ *From:* Dannon Baker [dannon.baker@gmail.com] *Sent:* Friday, April 11, 2014 4:57 PM
*To:* Wang, Xiaofei *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] how to delete datasets or save space on local galaxy
I replied too soon. To answer your second question, yes, that's how to use the cleanup scripts from the command line. Enabling the option from my previous email will allow users to *immediately* purge datasets without waiting on those cleanup scripts.
-Dannon
On Fri, Apr 11, 2014 at 5:55 PM, Dannon Baker <dannon.baker@gmail.com>wrote:
Hey, sure. The option you're looking for is "allow_user_dataset_purge", around line 650 or so.
Good luck!
-Dannon
On Fri, Apr 11, 2014 at 5:53 PM, Wang, Xiaofei <xfwang@ku.edu> wrote:
Hi Dannon,
Could you tell me how to edit the configure file?
What I see from here https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20... is how to use the command line, correct?
Thanks a lot!
Best,
Xiaofei ------------------------------ *From:* Dannon Baker [dannon.baker@gmail.com] *Sent:* Friday, April 11, 2014 4:42 PM *To:* Wang, Xiaofei *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] how to delete datasets or save space on local galaxy
Hi Xiaofei,
The (x) simply flags a dataset for deletion, it does not remove it from disk. This happens when the instance maintainers run cleanup scripts. If your instance is so configured, you can use the "Purge Deleted Datasets" option to immediately remove datasets from disk.
-Dannon
On Fri, Apr 11, 2014 at 5:33 PM, Wang, Xiaofei <xfwang@ku.edu> wrote:
Dear there,
May I ask a question which might be really simple?
How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it.
Thank you so much!
Best,
Xiaofei
___________________________________________________________ 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: http://lists.bx.psu.edu/
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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
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Carl Eberhard -
Dannon Baker -
Wang, Xiaofei