Installation

Python API

Installation of the phippery python package is available through

» pip install phippery

See also

for more information about how to contribute please see the Development page.

Alignments Pipeline

For running the Nextflow alignments pipeline, we maintain a Dockerfile, and host a pre-built public image on quay.io for convenience.

Note

Note that the quay image is pointed to by default in the pipeline configuration file – meaning if you have both Docker and Nextflow installed, you have everything you need to run the pipeline with --profile docker specified after the nextflow run command. The other option would be to pull, or build the image yourself, then run the pipeline within that container.

To install docker desktop (Desktop is just fine), on most unix OS:

» curl -fsSL https://get.docker.com -o get-docker.sh && sudo sh get-docker.sh

To test the Docker install:

» docker -v
Docker version 20.10.1, build 831ebea
» docker run docker/whalesay cowsay boo

To install Nextflow on most Unix OS:

» curl -s https://get.nextflow.io | bash

To test the Nextflow install:

» nextflow -v
nextflow version 20.04.1.5335

Streamlit App

We reccomend running streamlit through the quay public image we maintain.

Simply navigate to a directory where you have some .phip binary datasets and run

» docker run -p 8501:8501 -v $PWD:/app/data/ quay.io/matsengrp/phip-viz

for local installation

» git clone https://github.com/matsengrp/phip-viz.git
» (cd phip-viz && pip install -r requirements.txt)