cleanup_datasets.py with postgresql 8.1
All, My understanding is that the cleanup_datasets.py under scripts/cleanup_datasets should be compatible with 'older' versions of postgresql. I'm running 8.1 under CentOS 5. When I attempt to run the scripts, it fails to clean any data sets. From the logs, I'm noticing messages like: database_connection contains an unknown SQLAlchemy database dialect: postgresql In my universe_wsgi.ini I've defined the database_connection as: database_connection = postgresql://galaxy:********@localhost:5432/galaxydb and am confident it's working as Galaxy works fine, other than this problem with deleting older datasets. The pgcleanup.py script isn't an option, as it requires postgresql >=9.1. I noticed yet another version of cleanup_datasets.py under cron which looks like it might be compatible with postgres, but am leary of trying it as I'm not sure what it means by "1: database directory to clean". I'm not sure what directory to point this to, nor am I confident that just deleting data from the directory is the safest thing. Any suggestions on how to proceed? Thanks! Malcolm -- Malcolm Tobias 314.362.1594
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On 9/26/13 7:29 AM, Malcolm Tobias wrote:
All,
My understanding is that the cleanup_datasets.py under scripts/cleanup_datasets should be compatible with 'older' versions of postgresql. I'm running 8.1 under CentOS 5. When I attempt to run the scripts, it fails to clean any data sets. From the logs, I'm noticing messages like:
database_connection contains an unknown SQLAlchemy database dialect: postgresql
In my universe_wsgi.ini I've defined the database_connection as:
database_connection = postgresql://galaxy:********@localhost:5432/galaxydb
and am confident it's working as Galaxy works fine, other than this problem with deleting older datasets.
=9.1. I noticed yet another version of cleanup_datasets.py under cron which looks like it might be compatible with postgres, but am leary of
The pgcleanup.py script isn't an option, as it requires postgresql trying it as I'm not sure what it means by "1: database directory to clean". I'm not sure what directory to point this to, nor am I confident that just deleting data from the directory is the safest thing.
Any suggestions on how to proceed?
Thanks!
Malcolm
--
Malcolm Tobias
314.362.1594
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Malcolm Tobias