changing datasets file_path storage location
We are planning to change datasets directory location (file_path setting in universe_wsgi.ini) in our Galaxy installation. We will be moving existing datasets to the new directory location and updating XSendfile setting in Apache as well. I was wondering if there are any side effects that we should be considering before making this change. There are certain fields in the database (e.g. command_line in jobs table) which contain absolute path of datasets. Do we need to update any of these fields to make sure Galaxy is functional after file_path is changed? -- Thanks, Shantanu
Hi Shantanu, We are facing the same situation that migrating galaxy dataset to a new location is needed. I am wondering if you have done it successfully? Would be nice if you can share your experience with us. Cheers, D On Fri, Nov 30, 2012 at 9:21 AM, Shantanu Pavgi (Campus) <pavgi@uab.edu>wrote:
We are planning to change datasets directory location (file_path setting in universe_wsgi.ini) in our Galaxy installation. We will be moving existing datasets to the new directory location and updating XSendfile setting in Apache as well. I was wondering if there are any side effects that we should be considering before making this change. There are certain fields in the database (e.g. command_line in jobs table) which contain absolute path of datasets. Do we need to update any of these fields to make sure Galaxy is functional after file_path is changed?
-- Thanks, Shantanu ___________________________________________________________ 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:
Hi Derrick, We did that a year ago, while changing the mount point as part of setting up a shared file system between our Galaxy node and a cluster. Naturally we did a backup first, but I don't recall any issues from this. At the time Nate just advised not to have any jobs running at the time (and stop Galaxy of course). http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-February/008383.html Peter On Thursday, February 14, 2013, Derrick Lin wrote:
Hi Shantanu,
We are facing the same situation that migrating galaxy dataset to a new location is needed. I am wondering if you have done it successfully? Would be nice if you can share your experience with us.
Cheers, D
On Fri, Nov 30, 2012 at 9:21 AM, Shantanu Pavgi (Campus) <pavgi@uab.edu>wrote:
We are planning to change datasets directory location (file_path setting in universe_wsgi.ini) in our Galaxy installation. We will be moving existing datasets to the new directory location and updating XSendfile setting in Apache as well. I was wondering if there are any side effects that we should be considering before making this change. There are certain fields in the database (e.g. command_line in jobs table) which contain absolute path of datasets. Do we need to update any of these fields to make sure Galaxy is functional after file_path is changed?
-- Thanks, Shantanu ___________________________________________________________ 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:
Thanks Peter, Our data is backup and we are planning to shutdown the galaxy for moving data to the new place, change the file_path value in universe config, then start the galaxy again. My only concern is if the existing value of file_path get hard-coded in the database entries. Many thanks Derrick On Thu, Feb 14, 2013 at 8:47 PM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
Hi Derrick,
We did that a year ago, while changing the mount point as part of setting up a shared file system between our Galaxy node and a cluster. Naturally we did a backup first, but I don't recall any issues from this. At the time Nate just advised not to have any jobs running at the time (and stop Galaxy of course). http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-February/008383.html
Peter
On Thursday, February 14, 2013, Derrick Lin wrote:
Hi Shantanu,
We are facing the same situation that migrating galaxy dataset to a new location is needed. I am wondering if you have done it successfully? Would be nice if you can share your experience with us.
Cheers, D
On Fri, Nov 30, 2012 at 9:21 AM, Shantanu Pavgi (Campus) <pavgi@uab.edu>wrote:
We are planning to change datasets directory location (file_path setting in universe_wsgi.ini) in our Galaxy installation. We will be moving existing datasets to the new directory location and updating XSendfile setting in Apache as well. I was wondering if there are any side effects that we should be considering before making this change. There are certain fields in the database (e.g. command_line in jobs table) which contain absolute path of datasets. Do we need to update any of these fields to make sure Galaxy is functional after file_path is changed?
-- Thanks, Shantanu ___________________________________________________________ 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:
On Tuesday, February 19, 2013, Derrick Lin wrote:
Thanks Peter,
Our data is backup and we are planning to shutdown the galaxy for moving data to the new place, change the file_path value in universe config, then start the galaxy again.
My only concern is if the existing value of file_path get hard-coded in the database entries.
Many thanks Derrick
That's what I was worried about - but it seems everything was using relative paths :) Good luck, Peter
participants (3)
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Derrick Lin -
Peter Cock -
Shantanu Pavgi (Campus)