Installation¶

Typical installation time is 10 minutes.

Mac OS¶

Installation is via the terminal. Open Terminal.app (in Applications/Utilities).

Change to the directory where you want to put the source code of dnastack. For example:
```
cd /Users/myname
```

Download a copy of the source code, using the following command:

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

Note

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

Change to the newly created dnastack directory:
```
cd dnastack
```

Make a new python3 virtual environment, enable it and install the required packages:

python3 -m venv venv
source venv/bin/activate
pip install --upgrade pip
pip install -r requirements.txt

Run the program by following the Quick Demo page, or the more detailed instructions on the Running a Simulation page.
Done? Leave the virtual environment by typing:
```
deactivate
```

If you would like to make virtual gel images of simulation output (see page Virtual Gel Image), follow the additional steps below to install ImageMagick.

Install the Mac OS package manager Homebrew. This is necessary for installing ImageMagick in the next step. As described at https://brew.sh, install Homebrew by running command:
```
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
```
Install ImageMagick using homebrew:
```
brew install imagemagick
```

Linux Ubuntu¶

Installation is via the terminal.

Update your repositories and install git:

sudo apt-get update
sudo apt install git

Install pip for Python3:

sudo apt-get install build-essential libssl-dev libffi-dev python-dev
sudo apt install python3-pip

Use pip to install virtualenv:
```
sudo pip3 install virtualenv
```
If you would like to make virtual gel images of simulation output (see page Virtual Gel Image), install ImageMagick:
```
sudo apt install imagemagick
```
Follow the same instructions as for Mac OS above, up to Mac OS step 6.

Windows 10¶

We recommend installing a Linux Ubuntu environment on Windows, and then following the Linux installation instructions above. A Linux environment can be installed by using the Windows Subsystem for Linux (available on 64-bit versions of Windows 10). Alternatively, using Ubuntu under VirtualBox is another option.