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.

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

   mkdir origami
   cd origami
   

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

   git clone https://bitbucket.org/engineering-data-structure-organoids/revnano.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. Important: Rename the revnano repository to be upper case:

   mv revnano REVNANO
   

4. Get the source code for the contactmap Python module (this is a required helper module):

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

5. Make a python3 virtual environment and enable it:

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

6. 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 jupyterlab
   

When you have finished, your origami/ directory should contain three sub-directories:

contactmap/ REVNANO/ venv/

It is important that the REVNANO directory name is in upper case letters.

Now, REVNANO can be run either as a JupyterLab Python notebook (easiest and recommended) or from the command line. See Running as JupyterLab Notebook page or Running from Command Line page.

Note

For Raspberry Pi Linux, additional steps have to be taken to install the scipy library: sudo apt install libatlas-base-dev; sudo pip3 install pybind11; pip3 install scipy