Installation

The following installation 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.

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

   mkdir origami
   cd origami
   

2. Get the source code for the contactmap Python module :

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

Note

Running the git command on MacOS may require you to download developer tools. If these are not installed, a dialog box should prompt you to install them.

3. Make a python3 virtual environment and enable it:

   python3 -m venv venv
   source venv/bin/activate
   pip3 install --upgrade pip
   

4. Install the following libraries in the new Python 3 virtual environment you just set up:

   pip3 install networkx
   pip3 install scipy
   pip3 install matplotlib
   pip3 install scadnano
   

5. When you have finished, your origami/ directory should contain two sub-directories:

contactmap/ venv/

6. Change to the contactmap module:

   cd contactmap
   

Links on the Nucleic Acid Origami Contact Map index page (and in the left-hand menu) provide information on how to use each of the utility scripts.