Nextstrain – Zika

Nextstrain bioinformatics visualisation tool on Ubuntu server.

Nextstrain CLI

Zika tutorialNextstrain Zika / Zika Tutorial / Getting started

Server installation

Start and SSH to the Ubuntu Server

ssh user@

Add universe repository

sudo add-apt-repository universe

Update system

sudo apt update
sudo apt upgrade

Install Docker

sudo apt install apt-transport-https ca-certificates curl software-properties-common
curl -fsSL | sudo apt-key add -
sudo add-apt-repository "deb [arch=amd64] bionic stable"
sudo apt update
apt-cache policy docker-ce
sudo apt install docker-ce

Docker without sudo

sudo usermod -aG docker ${USER}
su - ${USER}
id -nG

Check Python version

python3 --version

Install python3 PIP

sudo apt install python3-pip

Install nextstrain-cli

pip3 install nextstrain-cli

Reboot or logout/login

Check Nextstrain setup has been installed

nextstrain check-setup

Nextstrain Output

A new version of nextstrain-cli, 1.5.0, is available!  You're running 1.4.1.

Upgrade by running:

    pip install --upgrade nextstrain-cli

Testing your setup…

✔ docker is installed
✔ docker run works

All good!

Nextstrain commands

usage: nextstrain [-h] {build,view,deploy,shell,update,check-setup,version} ...

Nextstrain command-line tool

optional arguments:
  -h, --help            show this help message and exit

    build               Run pathogen build
    view                View pathogen build
    deploy              Deploy pathogen build
    shell               Start a new shell in the build environment
    update              Updates your local image copy
    check-setup         Tests your local setup
    version             Show version information

Install Zika data tutorial

Clone zika setup

git clone

Change to zika directory

cd zika

Build zika

nextstrain build .

On/If error copy example_data/zika.fasta to data folder

cp example_data/zika.fasta data/

Build zika again

nextstrain build .

View in auspice (Front-end)

nextstrain view auspice/ --allow-remote-access

Auspice output

    The following datasets should be available in a moment:

> auspice@1.29.0 server /nextstrain/auspice
> node server.js

Auspice server started on port 4000
Serving compiled bundle from /dist
Local datasets sourced from /nextstrain/auspice/data can be accessed via "/local/..." URLs
Local narratives sourced from /nextstrain/auspice/local_narratives can be accessed via "/local/narratives/..." URLs

Successfully created local manifest
Successfully created live manifest
Successfully created staging manifest
Charon API request: /charon?request=mainJSON&url=/local/zika
	Success fetching v1 JSONs. Sending as a single JSON.

View datasets in the browser

Auspice start commands

usage: nextstrain view [-h] [--allow-remote-access] [--image <name>]
                       [--exec <prog>] [--auspice <dir>] [--docker-arg ...]

Visualizes a completed pathogen build in auspice, the Nextstrain web frontend.

The data directory should contain sets of files with at least two files:


The viewer runs inside a container, which requires Docker.  Run `nextstrain
check-setup` to check if Docker is installed and works.

positional arguments:
  <directory>           Path to pathogen build data directory

optional arguments:
  -h, --help            show this help message and exit
                        Allow other computers on the network to access the
                        website (default: False)

development options:
  These should generally be unnecessary unless you're developing build images.

  --image <name>        Container image in which to run the pathogen build
                        (default: nextstrain/base)
  --exec <prog>         Program to exec inside the build container (default:
  --auspice <dir>       Replace the image's copy of auspice with a local copy
                        (default: None)
  --docker-arg ...      Additional arguments to pass to `docker run` (default: