Problem with set_user_disk_usage.py script
I recently updated our server to the latest release and have just had a user who ran up a lot of space and isn’t seeing it come back when she purges her data. I’ve tried using the set_user_disk_usage.py script as I’ve previously done to resolve this but now it is failing with the following: (galaxy_env)[galaxy@galaxy scripts]$ ./set_user_disk_usage.py Loading Galaxy model... Traceback (most recent call last): File "./set_user_disk_usage.py", line 85, in <module> model, object_store, engine = init() File "./set_user_disk_usage.py", line 43, in init for key, value in config_parser.items( "app:main" ): File "/usr/lib64/python2.6/ConfigParser.py", line 565, in items raise NoSectionError(section) ConfigParser.NoSectionError: No section: ‘app:main' Do I need a newer python or is this a bug/regression? Shane Dr. Shane Sturrock Senior Scientist shane.sturrock@biomatters.com | P: +64 9 379 5064 BIOMATTERS
The script by default expects Galaxy config to be at config/galaxy.ini if you have Galaxy config in a diffferent place you can use the --config flag to specify path to it. The config location has been recently changed (from galaxy root folder and a different filename) - that is why the defaults are different then your setup. Sorry for the inconvenience. Martin On Mon, Jun 8, 2015 at 9:43 PM Shane Sturrock <shane@biomatters.com> wrote:
I recently updated our server to the latest release and have just had a user who ran up a lot of space and isn’t seeing it come back when she purges her data. I’ve tried using the set_user_disk_usage.py script as I’ve previously done to resolve this but now it is failing with the following:
(galaxy_env)[galaxy@galaxy scripts]$ ./set_user_disk_usage.py Loading Galaxy model... Traceback (most recent call last): File "./set_user_disk_usage.py", line 85, in <module> model, object_store, engine = init() File "./set_user_disk_usage.py", line 43, in init for key, value in config_parser.items( "app:main" ): File "/usr/lib64/python2.6/ConfigParser.py", line 565, in items raise NoSectionError(section) ConfigParser.NoSectionError: No section: ‘app:main'
Do I need a newer python or is this a bug/regression?
Shane
*Dr. Shane Sturrock*Senior Scientist shane.sturrock@biomatters.com | P: +64 9 379 5064 BIOMATTERS
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Thanks Martin, That solves it. What I ended up doing (since my install is pretty old now) was to symlink the galaxy-dist/universe_wsgi.ini to galaxy-dist/config/galaxy.ini and then the script started working. Shane
On 9/06/2015, at 3:15 pm, Martin Čech <marten@bx.psu.edu> wrote:
The script by default expects Galaxy config to be at config/galaxy.ini if you have Galaxy config in a diffferent place you can use the --config flag to specify path to it.
The config location has been recently changed (from galaxy root folder and a different filename) - that is why the defaults are different then your setup. Sorry for the inconvenience.
Martin
On Mon, Jun 8, 2015 at 9:43 PM Shane Sturrock <shane@biomatters.com <mailto:shane@biomatters.com>> wrote: I recently updated our server to the latest release and have just had a user who ran up a lot of space and isn’t seeing it come back when she purges her data. I’ve tried using the set_user_disk_usage.py script as I’ve previously done to resolve this but now it is failing with the following:
(galaxy_env)[galaxy@galaxy scripts]$ ./set_user_disk_usage.py Loading Galaxy model... Traceback (most recent call last): File "./set_user_disk_usage.py", line 85, in <module> model, object_store, engine = init() File "./set_user_disk_usage.py", line 43, in init for key, value in config_parser.items( "app:main" ): File "/usr/lib64/python2.6/ConfigParser.py", line 565, in items raise NoSectionError(section) ConfigParser.NoSectionError: No section: ‘app:main'
Do I need a newer python or is this a bug/regression?
Shane
Dr. Shane Sturrock Senior Scientist shane.sturrock@biomatters.com <mailto:shane.sturrock@biomatters.com> | P: +64 9 379 5064 BIOMATTERS
___________________________________________________________ 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/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>
Dr. Shane Sturrock Senior Scientist shane.sturrock@biomatters.com | P: +64 9 379 5064 BIOMATTERS
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Martin Čech -
Shane Sturrock