Installation

Pip

Note: Recommended

git clone https://github.com/satriobio/siren.git
cd siren
pip -e .

Conda

Note: Supports ROS driver for reading fast5 directly from s3

git clone https://github.com/satriobio/siren.git
cd siren
conda env create -f env.yaml

Docker

Note: Supports ROS driver for reading fast5 directly from s3

First build the image from the dockerfile.

git clone https://github.com/satriobio/siren.git
cd siren
docker build -t siren:latest .

Run as a container

# change $(pwd) with your data directory
docker run -it -v $(pwd):/data/ -p 5006:5006 siren:latest