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VM Setup

Below are a list of all commands run during the installation process on a clean VM.

1. Creating a new instance

Mostly defaults can be used, if in doubt follow official support.

  • Source: NeCTAR Ubuntu 20.04 LTS (Focal) amd64
  • Favour: m3.small
  • Security: Set the ssh, database, and egress_all security groups.
  • Ensure the security allows SSH access
  • You should add your SSH public key by using the import "Key Pair" option.

2. Instance setup

2a. Connecting for the first time

Connect to the instance using the root account:

ssh ubuntu@ip.address.of.server

2b. Creating your own account

You should now provision yourself (and others) new accounts:

sudo useradd -m -s /bin/bash USERNAME 
sudo passwd USERNAME
sudo usermod -aG sudo USERNAME

Add your SSH key to the list of authorised users to log in to that account:

sudo su - USERNAME
mkdir -p ~/.ssh
nano ~/.ssh/authorized_keys

2c. Increasing the swap size

By default, the swap size is ~100 MB for Nectar instances. The following increases it to 1 GB.

sudo swapoff -a
sudo fallocate -l 1G /swapfile
sudo chmod 600 /swapfile
sudo mkswap /swapfile
sudo swapon /swapfile
grep SwapTotal /proc/meminfo

2d. Setting the local date and time

sudo timedatectl set-timezone Australia/Brisbane
sudo timedatectl set-ntp on

3. Software installation

In order to run the instance the following software are required:

3a. Software configuration

The default subnet that Docker uses conflicts with the UQ VPN, you will need to update /etc/docker/daemon.json to be something like this:

{
  "default-address-pools" : [
    {
      "base" : "192.168.56.0/16",
      "size" : 24
    }
  ]
}

Once you're done, run systemctl restart docker

4. Clone the repository

Note: This requires that you have set up an SSH key with GitHub.

4a. Setting up an SSH key

ssh-keygen -t ed25519 -C "USER@EMAIL.COM"
eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_ed25519

4b. Adding the SSH key to your GitHub account

Follow the guide or add directly to your GitHub account.

cat ~/.ssh/id_ed25519.pub

4c. Cloning the repository

git clone git@github.com:Ecogenomics/db.gtdb.ecogenomic.org.git /var/db.gtdb.ecogenomic.org