How to update GenomeDepot from Python 3.10 to Python 3.12
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Delete (or rename) old virtual environment directory and create a new environment.
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Upgrade Python libraries
pip install --upgrade PyMySQL toyplot "django-q2==1.10.0" "biopython==1.87" "django==6.0.5" "django-admin-shortcuts==3.0.1" "django-cors-headers==4.9.0" "django-debug-toolbar==6.3.0" "openpyxl==3.1.5" "pandas==3.0.2" "plotly==6.7.0" "setuptools==82.0.1" "numpy==2.4.4"
Important! Do not upgrade parasail and toyplot libraries.
- Delete Jbrowse folder (in the external_tools folder) and re-install it:
curl -L -O https://github.com/GMOD/jbrowse/releases/download/1.16.11-release/JBrowse-1.16.11.zip
unzip JBrowse-1.16.11.zip
mv JBrowse-1.16.11 jbrowse
rm JBrowse-1.16.11.zip
cd jbrowse
./setup.sh
- Activate the virtual environment, go to the genomebrowser folder and run:
git pull
python manage.py migrate
python manage.py collectstatic
- Restart the web server
sudo systemctl restart apache2
- For Ubuntu users. If Python was upgraded with an OS upgrade, check the muscle version. If muscle v.5 was installed, replace it with muscle version 3.8 from https://drive5.com/muscle/downloads_v3.htm.
cd /usr/bin
sudo mv muscle muscle5
sudo ln -s muscle3.8.31_i86linux64 muscle
Posted Fri 08 May 2026, last updated Fri 08 May 2026 by aekazakov in Python (genomedepot, Python)