SMaHT Portal Pipeline Utilities

Documentation for smaht-pipeline-utils, a collection of utilities for deploying pipelines and interfacing with SMaHT portal infrastructure.

Contents

Pipeline Utils

• Install
  • PyPI
  • Source
• smaht_pipeline_utils
  • pipeline_deploy
• API

Contribute Pipelines

• Contribute a Pipeline
  • Building a Pipeline
    • Workflow Description Files
    • Docker Containers
    • Portal Objects
    • PIPELINE and VERSION Files
    • Examples
• Deploy Pipelines to AWS Environment
  • Setup an EC2 Machine
  • Install Docker
  • Install smaht_pipeline_utils
  • Set Up Credentials and Environmental Variables
    • AWS Auth Credentials
    • Portal Credentials
    • Target Account Information
  • Running the Deployment
  • Deploying SMaHT Pipelines
  • Uploading the Reference Files
  • Troubleshooting
    • Auth Errors
    • No Space Left on Device Errors

Pipeline’s Components

• Pipeline’s Repository Structure
• Portal Objects
  • File Format
    • Template
    • Fields Definition
  • File Reference
    • Template
    • Fields Definition
  • Software
    • Template
    • Fields Definition
  • Workflow
    • Template
    • General Fields Definition
    • Input Definition
    • Output Definition
  • Pipeline
    • Template
    • General Fields Definition
    • Workflows Definition
    • Input Definition