Re: [galaxy-dev] NFS configuration questions + NFS /etc/fstab configuration issue with AMI issue
Hey Scott, Glad you figured out the other two issues. Which file exactly are you editing that is getting overwritten? And when does it get overwritten? (on reboot, randomly, cluster terminate/start, etc?) -Dannon On Sun Jan 25 2015 at 12:20:12 PM Scott Jeschonek <scottj@averesystems.com> wrote:
Revising all of the below…
I figured out the configuration location and file system issues.
The only issue I have now is that my configured universe_wsgi.ini file is being overwritten with defaults. I modified it in the s3 bucket and locally but to no avail. Any ideas?
On Jan 24, 2015, at 12:17 PM, Scott Jeschonek <scottj@averesystems.com> wrote:
Hi,
I’m setting up a ‘local’ Galaxy server in AWS and had a few questions that I can’t seem to answer.
1. *Directory configuration in universe_wsgi.ini* — I want to use an NFS from another server. The purpose would be to deposit results there. I may also want to point to another NFS server as a centralized reference / index file system. I tried changing the path for the Indices setting and restarted Galaxy, but CloudMan is showing the file system as “error”. Basically I am trying to wrap my head around the steps to re-pointing to NFS mounts (is it just change the paths in universe_wsgi.ini then restart everything?)
2. *CloudMan AMI and fstab* — I’m using the latest AMI Cloudman instance and it seems to have an issue with NFS configurations in the fstab. I am not quite sure what is going on, the entry is correct. I’m able to manually mount the filesystems as well so the paths are correct. Is there something specific I need to change on that image?
Thanks in advance for any assistance!
Scott Jeschonek Avere Systems
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Hi Dannon, I tried a few things; /mnt/galaxy/galaxy-app has the universe_wsgi.ini file. I started there. It would be overwritten I then went to the s3 bucket and tried universe_wsgi.ini.cloud. Changed that. It too would eventually be overwritten with the defaults (plus the file above) I changed both of these as well, same result. So then I looked in cm.tar.gz and found more references to the files in python scripts and tried that. To no avail. I’m assuming some script is affecting this. What I did to work around this for now was to make a copy of universe_wsgi.ini to scot_universe_wsgi.ini and modified the local run.sh to call it instead. Scott
On Jan 28, 2015, at 9:56 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hey Scott,
Glad you figured out the other two issues. Which file exactly are you editing that is getting overwritten? And when does it get overwritten? (on reboot, randomly, cluster terminate/start, etc?)
-Dannon
On Sun Jan 25 2015 at 12:20:12 PM Scott Jeschonek <scottj@averesystems.com <mailto:scottj@averesystems.com>> wrote: Revising all of the below…
I figured out the configuration location and file system issues.
The only issue I have now is that my configured universe_wsgi.ini file is being overwritten with defaults. I modified it in the s3 bucket and locally but to no avail. Any ideas?
On Jan 24, 2015, at 12:17 PM, Scott Jeschonek <scottj@averesystems.com <mailto:scottj@averesystems.com>> wrote:
Hi,
I’m setting up a ‘local’ Galaxy server in AWS and had a few questions that I can’t seem to answer.
1. Directory configuration in universe_wsgi.ini — I want to use an NFS from another server. The purpose would be to deposit results there. I may also want to point to another NFS server as a centralized reference / index file system. I tried changing the path for the Indices setting and restarted Galaxy, but CloudMan is showing the file system as “error”. Basically I am trying to wrap my head around the steps to re-pointing to NFS mounts (is it just change the paths in universe_wsgi.ini then restart everything?)
2. CloudMan AMI and fstab — I’m using the latest AMI Cloudman instance and it seems to have an issue with NFS configurations in the fstab. I am not quite sure what is going on, the entry is correct. I’m able to manually mount the filesystems as well so the paths are correct. Is there something specific I need to change on that image?
Thanks in advance for any assistance!
Scott Jeschonek Avere Systems
___________________________________________________________ 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/ <https://lists.galaxyproject.org/>
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Dannon Baker -
Scott Jeshonek