seqslab-cli 3.3.2.post1

Atgenomix SeqsLab Command Line Tool

This package provides a unified command line interface to Atgenomix SeqsLab, a cloud-native biomedical informatics (BioMed IT) platform.

Table of Contents

1. Getting Started
   • Prerequisites
   • Install the SeqsLab CLI
   • Interactive Mode
   • CLI Mode
   • Basic Commands
2. Getting Help
3. Contributing
4. More Resources

Getting Started

Prerequisites

• Python 3.8 or later

• keyring

• dbus

• glib

• pkg-config

Detail to see Installation

Install the SeqsLab CLI

pip install seqslab-cli

Interactive Mode

This mode provides fish-style auto-completion functionality that is user-friendly, especially for beginners.

• Run interactive mode.

  seqslab
  

• Display the available commands.

  root> help
  

• End the current interactive mode session and return to the Linux shell.

  root> exit
  

CLI Mode

Through the use of subcommands, you can operate the SeqsLab CLI like any traditional Linux-based command-line utility.

seqslab -h

seqslab auth -h

Basic Commands

Authentication with the SeqsLab API

Regardless of the mode that you intend to use, you must sign in to authenticate the session. The SeqsLab CLI follows the OAuth 2.0 Device Authorization Grant (external URL) process.

Example (interactive mode):

• Specify the platform backend to be used when launching the SeqsLab CLI. The default value is azure.

  seqslab --backend azure
  

• Sign in to the SeqsLab API and obtain API tokens with a single command. By default, the sign-in process uses the Authorization Code Flow.

  root> auth signin
  

  Set the device-code argument to True. By default, the sign-in command uses the Device Code Flow for browserless systems.

  root>  auth signin device-code=True
  

• Obtain an API access token for interacting with SeqsLab API apps.

  root> auth token
  # use token in your request header, ex: Authorization: Bearer {access}
  

  Access tokens are persistently cached in the system-supported secret service (for example, Freedesktop Secret Service or macOS Keychain). As a result, valid access tokens can be used across multiple SeqsLab CLI sessions.

Help documentation

To view help documentation, use one of the following:

root> help

Getting Help

The best way to interact with our team is through GitHub. You can open an issue and choose from one of our templates for guidance, bug reports, or feature requests.

Please check for open similar issues before opening another one.

More Resources

• SeqsLab CLI Documentation

Contributing

The repository currently does not accept contributions but will eventually be opened to the community.