Skip to content

Install RIVET On Your Machine

Installing RIVET Backend using Docker on Linux

Install

Install Docker on your machine first.

For ease of use, the entire RIVET backend pipeline, including recombinant ranking, is contained within a pre-built public docker image.

Running RIVET Backend Locally On Your Machine

A RIVET backend job can be run locally on your machine. To launch a Docker shell, run the following two commands. 

docker run -it mrkylesmith/ripples_pipeline:latest
This will run an interactive Docker shell with the necessary RIVET environment.


Type the following help command to ensure your RIVET backend environment is configured correctly.

python3 rivet-backend.py --help

The wget command-line utility for downloading files from the internet (the necessary MAT, metadata and sequence files required as input to RIVET) is included in the Docker environment. Proceed to the next steps for running a RIVET backend job: Inferring Recombinants Using the RIVET Backend.


Running RIVET Backend On Google Cloud

We also provide the build-in option of running a parallelized RIVET job across a user specified number of Google Cloud Platform (GCP) machines.

Setup

If you would like to use GCP, please see the following docs for setting up an account with Google Cloud Platform: GCP Setup Docs

Important

Put your GCP service account key file (obtained following the docs linked above) in the corresponding location as the command below or update the location in the command below:

To launch a Docker shell using GCP, run the following two commands providing your GCP Authentication keys file.

KEY=~/.config/gcloud/<key_file.json>
docker run -it -e GOOGLE_APPLICATION_CREDENTIALS=/tmp/keys/<key_file.json> -v ${KEY}:/tmp/keys/<key_file.json>:ro mrkylesmith/ripples_pipeline:latest


Install RIVET Frontend Locally On Your Machine

Clone RIVET Repo Locally

git clone https://github.com/TurakhiaLab/rivet.git
cd rivet

Conda Install

Install

Install Conda on your machine first.

All the RIVET frontend dependencies have been added to Conda environment setup, that can be found in the install directory.


Run the following commands to activate the rivet Conda environment. 

conda env create -f install/rivet_env.yml
conda activate rivet

Type the following command to ensure your RIVET frontend environment is configured correctly, and then proceed to the next steps for using the RIVET frontend: Visualizing Your Results Using the RIVET Frontend

python3 rivet-frontend.py --help