Installation

The following instructions should work for both MacOS and Linux systems. Windows users are encouraged to install the Windows Subsystem for Linux (WSL) and then install the software inside Ubuntu Linux. Installation takes around 15 minutes.

  1. Make a directory origami/ somewhere on your computer, and change to it:

    mkdir origami
cd origami

  2. Get the source code for the scaffoldselector Python program, and two other required Python modules (contactmap and poolgen):

    git clone https://bitbucket.org/engineering-data-structure-organoids/scaffoldselector.git
git clone https://bitbucket.org/engineering-data-structure-organoids/contactmap.git
git clone https://bitbucket.org/engineering-data-structure-organoids/poolgen.git

  3. Make a Python3 virtual environment with the required modules installed in the origami/ directory, and activate it:

    python3 -m venv venv
source venv/bin/activate
pip install --upgrade pip
pip install matplotlib
pip install networkx
pip install scipy
pip install plotly
pip install pandas
pip install colorama

  4. Register an account on nupack.org, and download the (free) NUPACK Python module subject to the NUPACK software license agreement.

  5. Unzip the downloaded NUPACK zip file and move the folder into the origami/ directory. There should now exist a folder like origami/nupack-4.0.1.8/ (or a more up to date version number).

  6. Install the NUPACK Python module into the virtual environment (Note: Full installation instructions are in the NUPACK documentation, including extra notes for Apple Silicon Macs):

    python3 -m pip install -U nupack -f nupack-4.0.1.8/package

where nupack-4.0.1.8 is the name of the NUPACK Python module folder in the origami/ directory. Note that NUPACK can be a more up to date version than 4.0.1.8.

  1. Check NUPACK Python module is installed in the virtual environment:

    python3 -m pip show nupack

Name: nupack
Version: 4.0.1.8
Summary: Nucleic Acid Package

  2. The origami/ directory should now contain five sub-folders:

  • contactmap/

  • nupack-4.0.1.8/ (or a newer version)

  • poolgen/

  • scaffoldselector/

  • venv/

Installation is complete.