Moving Galaxy's installed folder
Hi all, Is there any official guidance on relocating a working Galaxy installation? Ours is currently up and running using PostreSQL, with everything installed under /opt/galaxy-dist I want to move this under /mnt/galaxy (a RAID partition which will be shared with a cluster). What needs to be done to make this move? In particular, I am worried there may be some absolute paths in the database which would need updating. In principle if only relative paths are used, everything will be fine... Any advice? Thanks, Peter
On Mon, Dec 12, 2011 at 4:09 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
Is there any official guidance on relocating a working Galaxy installation?
Ours is currently up and running using PostreSQL, with everything installed under /opt/galaxy-dist
I want to move this under /mnt/galaxy (a RAID partition which will be shared with a cluster).
What needs to be done to make this move? In particular, I am worried there may be some absolute paths in the database which would need updating. In principle if only relative paths are used, everything will be fine...
Any advice?
Thanks,
Peter
No advice? I guess I can just try it and see... Peter
On Dec 15, 2011, at 6:30 AM, Peter Cock wrote:
On Mon, Dec 12, 2011 at 4:09 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
Is there any official guidance on relocating a working Galaxy installation?
Ours is currently up and running using PostreSQL, with everything installed under /opt/galaxy-dist
I want to move this under /mnt/galaxy (a RAID partition which will be shared with a cluster).
What needs to be done to make this move? In particular, I am worried there may be some absolute paths in the database which would need updating. In principle if only relative paths are used, everything will be fine...
Any advice?
Thanks,
Peter
No advice? I guess I can just try it and see…
Hey Peter, Sorry we missed this one. I believe as long as you are not trying to move it while there are jobs running, you should be fine. --nate
Peter ___________________________________________________________ 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 Wed, Feb 1, 2012 at 5:12 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Dec 15, 2011, at 6:30 AM, Peter Cock wrote:
On Mon, Dec 12, 2011 at 4:09 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
Is there any official guidance on relocating a working Galaxy installation?
Ours is currently up and running using PostreSQL, with everything installed under /opt/galaxy-dist
I want to move this under /mnt/galaxy (a RAID partition which will be shared with a cluster).
What needs to be done to make this move? In particular, I am worried there may be some absolute paths in the database which would need updating. In principle if only relative paths are used, everything will be fine...
Any advice?
Thanks,
Peter
No advice? I guess I can just try it and see…
Hey Peter,
Sorry we missed this one. I believe as long as you are not trying to move it while there are jobs running, you should be fine.
--nate
Great - that's what I was hoping. We've changed some things on the cluster to prepare for this - e.g. our Galaxy server is now a proper SGE submit host, so I'm not quite ready to move the production server... still a few little things to sort out first, e.g. https://bitbucket.org/galaxy/galaxy-central/issue/713 Peter
On Feb 1, 2012, at 12:16 PM, Peter Cock wrote:
On Wed, Feb 1, 2012 at 5:12 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Dec 15, 2011, at 6:30 AM, Peter Cock wrote:
On Mon, Dec 12, 2011 at 4:09 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
Is there any official guidance on relocating a working Galaxy installation?
Ours is currently up and running using PostreSQL, with everything installed under /opt/galaxy-dist
I want to move this under /mnt/galaxy (a RAID partition which will be shared with a cluster).
What needs to be done to make this move? In particular, I am worried there may be some absolute paths in the database which would need updating. In principle if only relative paths are used, everything will be fine...
Any advice?
Thanks,
Peter
No advice? I guess I can just try it and see…
Hey Peter,
Sorry we missed this one. I believe as long as you are not trying to move it while there are jobs running, you should be fine.
--nate
Great - that's what I was hoping.
We've changed some things on the cluster to prepare for this - e.g. our Galaxy server is now a proper SGE submit host, so I'm not quite ready to move the production server... still a few little things to sort out first, e.g. https://bitbucket.org/galaxy/galaxy-central/issue/713
I suspect that you are going to encounter more problems with the local and cluster mountpoints being different. Is it not possible to mount it at /data/galaxy on the Galaxy server? --nate
Peter
On Wed, Feb 1, 2012 at 5:44 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Feb 1, 2012, at 12:16 PM, Peter Cock wrote:
We've changed some things on the cluster to prepare for this - e.g. our Galaxy server is now a proper SGE submit host, so I'm not quite ready to move the production server... still a few little things to sort out first, e.g. https://bitbucket.org/galaxy/galaxy-central/issue/713
I suspect that you are going to encounter more problems with the local and cluster mountpoints being different. Is it not possible to mount it at /data/galaxy on the Galaxy server?
It is mounted at /data/galaxy on the Galaxy server, but at /mnt/galaxy on the cluster, but I see what you mean. The two machines are administered by different people, but we can probably find a common mount point if trying to do this with symlinks is really not recommended. Thanks, Peter
On Feb 1, 2012, at 12:49 PM, Peter Cock wrote:
On Wed, Feb 1, 2012 at 5:44 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Feb 1, 2012, at 12:16 PM, Peter Cock wrote:
We've changed some things on the cluster to prepare for this - e.g. our Galaxy server is now a proper SGE submit host, so I'm not quite ready to move the production server... still a few little things to sort out first, e.g. https://bitbucket.org/galaxy/galaxy-central/issue/713
I suspect that you are going to encounter more problems with the local and cluster mountpoints being different. Is it not possible to mount it at /data/galaxy on the Galaxy server?
It is mounted at /data/galaxy on the Galaxy server, but at /mnt/galaxy on the cluster, but I see what you mean. The two machines are administered by different people, but we can probably find a common mount point if trying to do this with symlinks is really not recommended.
Symlinks should be fine, as well. I would make the Galaxy server's path "real", however, and use symlinks on the cluster. --nate
Thanks,
Peter
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Nate Coraor -
Peter Cock