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.

Make a directory for installation and change to it, for example:
```
mkdir origami
cd origami
```
Make a Python3 virtual environment in the origami/ directory, activate it, and install necessary Python modules:
```
python3 -m venv venv
source venv/bin/activate
pip install --upgrade pip
pip install colorama
```

Clone the following repositories into the origami/ directory:

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

The origami/ directory should have folders contactmap/, poolgen/ and venv/.
To perform a quick test, change to the poolgen/ directory…
```
cd poolgen
```
…and generate 200 random DNA sequences of 100nt each, sending output to _assets/random.csv:
```
python3 generate.py 200 randomdna 100 random.csv
```

Basic installation is complete! See the documentation page Generate Sequences.

Advanced Installation

If you would like to check if primer dimers are a problem in PCR Primer Check, then the NUPACK Python module also needs to be installed as follows:

Change to the directory where the above installation was done:
```
cd origami
```
Register an account on nupack.org, and download the (free) NUPACK Python module subject to the NUPACK software license agreement.
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/.
When in the origami/ directory, activate the Python virtual environment:
```
source venv/bin/activate
```
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 in the origami/ directory.

Check that NUPACK Python module is installed in the virtual environment:
```
python3 -m pip show nupack
```