Install RIVET On Your Machine
Installing RIVET Backend using Docker
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 shell with the necessary RIVET environment.
Type the following command to ensure your RIVET backend environment is configured correctly, and then 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
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.
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