I have a Galaxy 19.09 installation I need to upgrade to 20.05. It is running on Ubuntu 18.04.2 LTS. I also want to update it to use Python3 (currently running with Python 2.7). I was generally following the procedure from “https://galaxyproject.org/admin/maintenance/” under section " General Update Procedures" but I’m worried this may be outdated. Below I’ve listed my planned steps. I’m hoping someone more knowledgeable can let me know if I’m following the wrong instructions.
- clone existing prod instance (version 19.09) using tar/gzip
- clone PostgreSQL database using “CREATE DATABASE galaxy_prod2 WITH TEMPLATE galaxy OWNER galaxy;”
- update galaxy.yml for cloned installation and change database_connection parameter to use new database called galaxy_prod2.
- Next upgrade to 20.01 so I can step my way to latest version: “git fetch origin && git checkout release_20.01 && git pull --ff-only origin release_20.01”
- then follow instructions on page “https://galaxyproject.org/admin/maintenance/” under section " General Update Procedures".
- I’m especially unclear whether I need to execute steps #3, #4, and #8.
- assuming that all works, then use git to get latest version 20.05 and follow same instructions.
- upgrade from Python 2.7 to Python 3
I tried upgrading Python first but ran into trouble so I assumed I had to upgrade Galaxy first to latest version. I followed these steps for the Python upgrade before attempting to upgrade Galaxy.
I followed these instructions:
- I removed .venv from base galaxy install directory
- Followed Step #3: set this in .bash_profile and in the current window: export GALAXY_PYTHON=/usr/bin/python3
- created symbolic link to python3 and added at beginning of path
- verified new correct version using “python --version” <-- now shows 3.6.8
- followed step #4 and issued this: “rm -rf /path/to/galaxy/database/compiled_templates/” <-- updated for my env
- started galaxy: now when Galaxy started it rebuilt .venv from Python 2.7 instead of 3.6.8.
Obviously the Python upgrade did not work. Something under Galaxy is holding onto 2.7 and I’m not sure what.
Thanks in advance for any help or advice.