AusTrakka CLI

Command line interface for AusTrakka V2.

Getting started with the CLI

The AusTrakka CLI is a command-line interface for interacting with the AusTrakka platform. To use it, you will need an AusTrakka account which grants the relevant roles and permissions in any organisation or project you wish to interact with.

The CLI can be used for several purposes, including:

• Submitting sequence data
• Submitting metadata (sample, sequence and epidemiological metadata)
• Retrieving data for analysis
• Uploading analysis results (trees and analysis-derived metadata)

Note that currently, sequence data can only be submitted using the CLI, and cannot be submitted via the web interface.

Installation

The CLI requires Python to run. If you would like to use conda to install Python, install the CLI, and save the necessary environment variables, you can first install either Miniforge (https://github.com/conda-forge/miniforge) or Miniconda (https://docs.conda.io/en/latest/miniconda.html). We recommend Miniforge for most users.

Note that as a part of installing the CLI, you will need to set the AT_URI environment variable. This will be provided by the AusTrakka team.

Install into a conda environment (optional but recommended)

If you wish to create a conda environment named austrakka with the necessary environment variables set and the at-login alias, run:

conda create -n austrakka python=3.12
conda activate austrakka
python -m pip install austrakka
conda env config vars set AT_URI=[VALUE]
mkdir -p ${CONDA_PREFIX}/etc/conda/activate.d
echo "alias at-login=\"export AT_TOKEN=\\\$(austrakka auth user)\"" > ${CONDA_PREFIX}/etc/conda/activate.d/austrakka-alias.sh

Note that the last two lines are valid only for Linux/Mac and will not work on Windows. These lines create an alias at-login in the conda environment, which will log you in to the CLI.

You can then use

conda activate austrakka
at-login

in order to use the CLI. See User Authentication below for alternative login methods.

Install without conda

If you are using Windows, and are not a WSL or Powershell user, it is strongly recommended to use conda (see above).

To install without conda, simply install with

python -m pip install austrakka

You will need to set the environment variable AT_URI. You can do this by running:

Mac / Linux

export AT_URI=[VALUE]

You may wish to add this to your .bashrc or .zshrc file.

Windows: Powershell

$Env:AT_URI = [VALUE]

To use the CLI, you must log in by setting the AT_TOKEN environment variable using the austrakka auth user command (see User Authentication, below).

Mac / Linux

You may wish to configure a login command for convenience:

alias at-login="export AT_TOKEN=\$(austrakka auth user)"

You may wish to add this to your .bashrc or .zshrc file.

Windows: Powershell

You may wish to configure a login command for convenience:

Function at-login { $Env:AT_TOKEN = austrakka auth user }

You may wish to add this to your config.ps1 file.

Updating the CLI

To update to the latest version, run

python -m pip install --upgrade austrakka

If you have installed the CLI into a conda environment, you should first activate it with conda activate austrakka:

conda activate austrakka
python -m pip install --upgrade austrakka

Logging in

Before you can use the CLI, you must log in as described below, to allow the CLI to use your AusTrakka credentials. Your authorisation will expire after a period and you will need to log in again.

User Authentication

Most users will want to log in to the CLI this way.

For any of these methods, you should be directed to log in via a browser and enter a code to authorise the CLI. This browser-based login uses your institutional credentials, i.e. the same credentials you use to log in to the AusTrakka web interface, and will authenticate you via your institution's identity provider.

Mac / Linux

If you have configured a login command as described above, you can simply run

at-login

Otherwise, you will need to set the AT_TOKEN environment variable. In a Mac or Linux environment you can run:

export AT_TOKEN=$(austrakka auth user)

Windows: Powershell

$Env:AT_TOKEN = austrakka auth user

Windows: Cmd

Set the AT_TOKEN environment variable by first running

austrakka auth user

to obtain a token string, and then running

set AT_TOKEN=<output of previous command>

:w to set the environment variable.

Process Authentication

This authentication mode is intended for long-term automated processes. Most users will not need it.

To authenticate a process, you'll need to set the following environment variables:

AT_AUTH_PROCESS_ID
AT_AUTH_PROCESS_SECRET

Values for AT_AUTH_PROCESS_ID and AT_AUTH_PROCESS_SECRET will be provided to you by the AusTrakka team. Note that the secret value is sensitive.

Once these variables are set, run the following to authorise:

Mac/Linux

export AT_TOKEN=$(austrakka auth process)

Windows: Powershell

$Env:AT_TOKEN = austrakka auth process

Windows: Cmd

Set the AT_TOKEN environment variable by first running

austrakka auth process

to obtain a token string, and then running

set AT_TOKEN=<output of previous command>

to set the environment variable.

Using the CLI

The CLI has a subcommand structure. Run

austrakka -h

to see available subcommands.

Run e.g.

austrakka metadata -h

to see available commands to manipulate metadata.

Run e.g.

austrakka metadata add -h

to see the usage of the metadata add command to upload metadata files.

Environment Variables Reference

Name	Description
AT_TOKEN	AusTrakka auth token
AT_URI	URI for API endpoint
AT_LOG_LEVEL	Level of logging
AT_LOG	Set to file to redirecting logging to a temp file
AT_CMD_SET	Set to austrakka-admin to display admin commands (these will not actually run successfully unless you have an appropriate role on the server)
AT_SKIP_CERT_VERIFY	Skips verification of the cert used by the AusTrakka backend
AT_SKIP_VERSION_CHECK	Skips checking of new CLI version
AT_USE_HTTP2	Uses HTTP2 (experimental)

All commands require AT_URI and AT_TOKEN to be set, except for auth commands.

Project Structure

Each logical component of the system has its own package under austrakka/. Eg. austrakka/job. Components that are children of another component are nested beneath. Eg. austrakka/job/instance.

Each component package contains the following files:

File	Purpose
__init__.py	Contains the Click commands offered by the component. Note that even if a component does not have any commands associated with it, this file must exist for the final build to include it.
funcs.py	Any functions associated with the component.
opts.py	Click command line options associated with the component. Defined here so they can be reused across the CLI. Eg. --species is used for multiple commands. The species CLI option is defined here and imported to all commands that use it.
enums.py	Any enumerations associated with the component.