Poretitioner

Poretitioner is an application for reading reporter proteins from nanopore sensors.

Getting Started: Users

Here's how to use Poretitioner out of the box.

• Download Docker, if you don't have it already.

• Download the Docker image here.

• From the directory you downloaded the docker image to, run

docker load < docker_poretitioner.tar.gz

• Now you're ready to use poretitioner. Run

docker run poretitioner:latest

Getting Started: Developers

If you're interested in contributing to Poretitioner, here's how to get started:

• Clone the project

git clone https://github.com/uwmisl/poretitioner.git

• Navigate to the repository cd poretitioner

• Run bash ./bootstrap_dev.sh

  • This will set you up with Nix (our package manager) and all other developer dependencies needed to build and contribute to the project

• You're all set!

Build the application

• Run nix-build -A app
• The poretitioner binary now exists at ./result/bin/poretitioner
• Run

./result/bin/poretitioner

Build a docker image of the application

Docker images can only be built on Linux machines.

• Run

docker_image=$(nix-build -A docker)

• The environment variable docker_image now contains a path to the docker image, copy this file wherever you need it.

docker load < ${docker_image}

Uninstall

To uninstall Nix and this project's dependencies (for example, if you want to wipe your workspace totally clean and start over), run

./boostrap_dev uninstall

On Mac OS 10.15 (Catalina) and up, this will require some additional steps that the script will elaborate on.

How it works

The full paper, Multiplexed direct detection of barcoded protein reporters on a nanopore array, describes the application in detail. Here's a summary in GIF form: