Any feedback on this? Our local instance of Galaxy is ready to "go live" and this is one of the remaining issues keeping us from more wide-spread usage.
Can anyone confirm that I should be using scripts/cleanup_datasets/cleanup_datasets.py when I'm using postgresql? Are there any limits on the versions of postgresql? Thanks in advance, Malcolm On Thursday 26 September 2013 17:16:16 Jennifer Jackson wrote: > Posting to galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu> to give the > question better exposure to the development community. > Please remove the galaxy-u...@bx.psu.edu<mailto:galaxy-u...@bx.psu.edu> > mailing list from all replies - we want to avoid double posts. > > > For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > 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. > > 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 > > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > -- > Jennifer Hillman-Jackson > http://galaxyproject.org > -- Malcolm Tobias 314.362.1594
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