Installation

Prerequisites

• Install Anaconda

• Install git

Linux

• Download the SCOUT repository directly from Github or using git:

git clone https://github.com/chunglabmit/scout.git

• Install the scout conda environment:

cd scout/
conda env create -f environment.yml

• Activate the scout environment and install SCOUT in editable mode:

conda activate scout
pip install -r requirements.txt
pip install -e .

Windows

Note: Windows users need to use the “Anaconda Prompt” terminal if conda is not available from your PATH variable.

• Download the SCOUT repository directly from Github or using git:

git clone https://github.com/chunglabmit/scout.git

• Create a scout conda environment:

conda create -n scout python=3.6

• Install required dependencies:

cd scout/
conda activate scout
pip install -r requirements.txt

Note: Some dependencies require a bit more work to install on Windows. We may include a Dockerfile in the future.

MacOS

SCOUT has not been tested with MacOS, but the Linux install instructions may work.

Updates

Installing SCOUT in editable mode makes updating easy. You can simply pull the latest version from Github:

git pull  # Run inside scout installation folder