genomenet / model_recipes

GenomeNet conda recipes

GenomeNet Labs

This repository provides instructions and configurations to set up GenomeNet Labs on a server using EC2 instance, Nginx, and Jobson.

Info

The server runs on an AWS EC2 t2.medium instance (Ubuntu 22.04.2 LTS) with a 40GB disk and belongs to the webappjobson security group.

Installation and Configuration

Follow the steps below to install necessary dependencies and set up GenomeNet Labs:

sudo apt-get update
sudo apt-get install -y default-jre nginx python3-pip runc

Clone the repo

git clone https://github.com/GenomeNet/Labs

Copy the UI to the www folder

sudo cp -r www/genomenet /var/www/genomenet

Maybe adjust sites-available

sudo cp jobson-ui /etc/nginx/sites-available/jobson-ui
cd /etc/nginx/sites-enabled
sudo ln -s ../sites-available/jobson-ui jobson-ui
sudo rm default
sudo nginx -s reload

Start the job submission server

cd server-job-processing

./install_conda_envs.sh # install conda environments

echo "export PATH=\$PATH:$(pwd)/server-job-processing
/jobson-nix-1.0.13/bin" >> ~/.bashrc

# Confirm that Jobson is installed correctly by checking the help command jobson -h

jobson serve config.yml # Start the server

If jobson is not running

# Install Jobson
wget https://github.com/adamkewley/jobson/releases/download/1.0.13/jobson-nix-1.0.13.tar.gz
tar xvf jobson-nix-1.0.13.tar.gz
echo "export PATH=\$PATH:/home/ubuntu/jobson-nix-1.0.13/bin" >> ~/.bashrc
source ~/.bashrc

Start the model upload server

cd server-model-processing
npm start