Trouble maintaining Galaxy config on cloud instance

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Trouble maintaining Galaxy config on cloud instance

David Kovalic
Hi,

I am trying to change the ftp dir (and some other modifications) vs. the standard Galaxy Cloudman config.

When I modify the appropriate line in /mnt/galaxy/galaxy-app/universe_wsgi.ini on my running cloud instance: my changes disappear when I terminate/restart the cluster.

When I modify universe_wsgi.ini.cloud and upload to the S3 bucket the file gets overwritten by the default when I restart the cluster...

I can't find anywhere on the net which file I need to modify in order to have config changes persist.

Any help would be greatly appreciated.

Thanks,

David

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Re: Trouble maintaining Galaxy config on cloud instance

Enis Afgan-3
Hi David,
I'm afraid some of that is embedded in CloudMan's code. Given you're restarting your cluster, you can unpack cm.tar.gz from your cluster's bucket (you can find this on CloudMan's Admin page) and edit cm/util/galaxy_conf.py to change the value for desired variables (under populate_galaxy_paths method). Once you're done, just create the tarball of the source again and upload it back to your cluster's bucket.

Let us know if you that doesn’t work for you. We're working on a better solution for this.

Best,
Enis

On Mon, Mar 30, 2015 at 5:58 PM, David Kovalic <[hidden email]> wrote:
Hi,

I am trying to change the ftp dir (and some other modifications) vs. the standard Galaxy Cloudman config.

When I modify the appropriate line in /mnt/galaxy/galaxy-app/universe_wsgi.ini on my running cloud instance: my changes disappear when I terminate/restart the cluster.

When I modify universe_wsgi.ini.cloud and upload to the S3 bucket the file gets overwritten by the default when I restart the cluster...

I can't find anywhere on the net which file I need to modify in order to have config changes persist.

Any help would be greatly appreciated.

Thanks,

David

___________________________________________________________
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Re: Trouble maintaining Galaxy config on cloud instance

David Kovalic
Enis,

Thanks for the pointers, I tried this and it didn't work for me. After I modified cm/util/galaxy_conf.py CM would no longer successfully start up my cluster. I suspect user-induced-syntax-error at my end when I modified the file, I am a perl guy and my python is not so great :(

What I did that worked was to change the default ftp directory to a symbolic link pointing to my desired location. After this the UI can see and access the file system I want to use.

Obviously it would be fantastic to have a slick mechanism to specify and persist any valid galaxy configuration mods, in any case I am good to go right now.

Thanks, your help is greatly appreciated!

David

On Mon, Mar 30, 2015 at 8:52 PM, Enis Afgan <[hidden email]> wrote:
Hi David,
I'm afraid some of that is embedded in CloudMan's code. Given you're restarting your cluster, you can unpack cm.tar.gz from your cluster's bucket (you can find this on CloudMan's Admin page) and edit cm/util/galaxy_conf.py to change the value for desired variables (under populate_galaxy_paths method). Once you're done, just create the tarball of the source again and upload it back to your cluster's bucket.

Let us know if you that doesn’t work for you. We're working on a better solution for this.

Best,
Enis

On Mon, Mar 30, 2015 at 5:58 PM, David Kovalic <[hidden email]> wrote:
Hi,

I am trying to change the ftp dir (and some other modifications) vs. the standard Galaxy Cloudman config.

When I modify the appropriate line in /mnt/galaxy/galaxy-app/universe_wsgi.ini on my running cloud instance: my changes disappear when I terminate/restart the cluster.

When I modify universe_wsgi.ini.cloud and upload to the S3 bucket the file gets overwritten by the default when I restart the cluster...

I can't find anywhere on the net which file I need to modify in order to have config changes persist.

Any help would be greatly appreciated.

Thanks,

David

___________________________________________________________
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/