Welcome to pyriandx’s documentation!

pyriandx

pyriandx is CLI client and Python SDK/Library for PierianDx Clinical Genomics Workspace (CGW) web services – https://umccr.github.io/pyriandx/

• Test Coverage

• PyDoc

• https://github.com/umccr/pyriandx

TL;DR

• Install through pip like so:

  pip install pyriandx
  

• Export PDX_ environment variables:

  export PDX_USERNAME=<YOUR_PierianDx_CGW_LOGIN_EMAIL>
  export PDX_PASSWORD=<YOUR_PierianDx_CGW_LOGIN_PASSWORD>
  export PDX_INSTITUTION=<ASK_YOUR_PierianDx_CGW_ACCOUNT_MANAGER>
  export PDX_BASE_URL=https://app.pieriandx.com/cgw-api/v2.0.0
  

• Print CLI command help:

  pyriandx version
  pyriandx help
  pyriandx case help
  pyriandx list help
  pyriandx create help
  pyriandx upload help
  pyriandx run help
  pyriandx job help
  pyriandx poll help
  pyriandx report help
  

• More examples/tutorials available at User Guide

License

MIT License and DISCLAIMER

Contents:

• USER GUIDE
  • Prerequisite
  • Command Concept
  • Printing Help
  • Getting a Case
  • Listing all Cases
  • Accession a New Case
  • Uploading Case Files
  • Sequencer Run
  • Informatics Job
  • Polling Job Status
  • Download Analysis Report
  • Case Assignment
  • Issues
• DEVELOPER GUIDE
  • Project Setup
  • Running Test Suite
  • Documentation
• CHANGE LOG
  • 0.3.0
  • 0.2.0

Indices and tables

• Index

• Module Index

• Search Page