Cadnano2 DNA Origami Design Software

Overview

Cadnano is computer-aided design software for DNA origami nanostructures. The original citation is here.

Installation

macOS

• Install homebrew
• Install python3: brew install python3
• Create a virtualenv: python3 -m venv ~/virtualenvs/cn24x
• Activate virtualenv: source ~/virtualenvs/cn24x/bin/activate
• Install via pip: pip3 install cadnano2

Linux

• Create a virtual env: python3 -m venv ~/virtualenvs/cn24x
• Activate the venv: source ~/virtualenvs/cn24x/bin/activate
• Install from PyPI: pip3 install cadnano2

Windows (tested for Python 3.10.4)

• Download and install latest python3
• Use "Manage app execution aliases" to disable launching "App Installer" via any python executables.
• Add python app folder to your system path, e.g. C:\Users\shawn\AppData\Local\Programs\Python\Python310\
• Add scripts folder to your system path, e.g. C:\Users\shawn\AppData\Local\Programs\Python\Python310\Scripts\
• Open command prompt (cmd.exe) and confirm you can run "python" and "pip".
• Install Cadnano via pip: pip install cadnano2

Running

macOS or Linux

• Open the Terminal
• (macOS or Linux) Activate virtual env:
  • source ~/virtualenvs/cn24x/bin/activate
• Run the app: cadnano2

Windows

• Open the Command Prompt
• Run the app: cadnano2

macOS alias

• Add to ~/.zprofile: alias cn2="source ~/virtualenvs/cn24x/bin/activate && cadnano2"
• Open new Terminal and run: cn2

Upgrading

• Open the Terminal
• Activate virtual env: source ~/virtualenvs/cn24x/bin/activate
• Upgrade via pip: pip install --upgrade cadnano2

Development

Setup a dev environment (Mac or Linux)

• Create a virtualenv: python3 -m venv ~/virtualenvs/cn24dev
• Activate virtualenv: source ~/virtualenvs/cn24dev/bin/activate
• Install PyQt6: pip install pyqt6
• Clone repo: git clone git@github.com:douglaslab/cadnano2.git
• Change directory: cd cadnano2
• Make desired code edits
• Build and install: python setup.py install
• Test: cadnano2
• Repeat previous 3 steps as needed

Setup a dev environment (Windows)

• Install venv: pip install virtualenv
• Create a virtualenv: python -m venv virtualenvs\cn24dev (e.g. in %homepath%)
• Activate virtualenv: virtualenvs\cn24dev\Scripts\activate
• Install PyQt6: pip install pyqt6
• Clone repo: git clone git@github.com:douglaslab/cadnano2.git
• Change directory: cd cadnano2
• Make desired code edits
• Build and install: python setup.py install
• Test: cadnano2
• Repeat previous 3 steps as needed

Build new dist and upload to PyPi

• pip install build twine <- install build and twine
• cd /path/to/cadnano2/
• python3 -m build creates dist/cadnano2-x.y.z.tar.gz and cadnano2-x.y.z-py3-none-any.whl
• python3 -m twine upload dist/cadnano2-x.y.z*

Version notes

This version of Cadnano2 is maintained by the Douglas Lab. It is derived from cadnano/cadnano2.

If you wish to use the Cadnano Python API for scripting, see cadnano2.5.

License

This version of Cadnano2 is available under the MIT License. GUI code that uses PyQt6 is GPLv3 as required by Riverbank Computing.