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?
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 deleted?
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