On Mar 22, 2013, at 11:56 AM, Lance Parsons wrote:
> I have been running a Galaxy server for our sequencing researchers for a
> while now and it's become increasingly successful. The biggest resource
> challenge for us has been, and continues to be disk space. As such, I'd like
> to implement some additional cleanup scripts. I thought I run a few questions
> by this list before I got too far into things.
> In general, I'm wondering how to implement updates/additions to the cleanup
> system that will be in line with the direction that the Galaxy project is
> headed. The pgcleanup.py script is the newest piece of code in this area
> (and even adds cleanup of exported histories, which are absent from the older
> cleanup scripts). Also, the pgcleanup.py script uses a "cleanup_event" table
> that I don't believe is used by the older cleanup_datasets.py script.
> However, the new pgcleanup.py script only works for Postgres, and worse, only
> for version 9.1+. I run my system on RedHat (CentOS) and thus we use version
> 8.4 of Postgres. Are there plans to support other databases or older
> versions of Postgres?
pgcleanup.py makes extensive use of Writable CTEs, so there is not really a way
to port it to older versions. For 8.4 or MySQL, you can still use the older
> I'd like to implement a script to delete (set the deleted flag) for certain
> datasets (e.g. raw data imported from our archive, for old, inactive users,
> etc.). I'm wondering if it would make sense to try and extend pgcleanup.py
> or cleanup_datasets.py. Or perhaps it would be best to just implement a
> separate script, though that seems like I'd have to re-implement a lot of
> boilerplate code for configuration reading, connections, logging, etc. Any
> tips on generally acceptable (supported) procedures for marking a dataset as
You could probably reuse a lot of the code from either of the cleanup scripts
> Of course, I'll make any of the enhancements available (and would be happy to
> submit pull requests if there is interest).
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
> 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:
> To search Galaxy mailing lists use the unified search at:
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:
To search Galaxy mailing lists use the unified search at: