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Category: Python

How to update GenomeDepot from Python 3.10 to Python 3.12

  1. Delete (or rename) old virtual environment directory and create a new environment.

  2. 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.

  1. 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
  1. Activate the virtual environment, go to the genomebrowser folder and run:
git pull
python manage.py migrate
python manage.py collectstatic
  1. Restart the web server
sudo systemctl restart apache2
  1. 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)