GeneFlow Documentation

Version: 2.3.0

GeneFlow (GF) is a light-weight platform-agnostic workflow engine for scientific computing.

• Background and Introduction
• Install GeneFlow
  • Requirements
    • Install Dependencies in Ubuntu/Debian Systems
    • Install Dependencies in CentOS/RHEL Systems
    • Python Modules
  • Prepare the CDC Environment to run GeneFlow
    • Prepare the CDC Environment and Load the GeneFlow Module
    • Prepare Agave in the CDC Environment
  • Install GeneFlow in a General Linux Environment
    • Install GeneFlow using a Python Virtual Environment
    • Prepare Agave in a General Linux Environment
• GeneFlow Usage
  • GeneFlow Command-Line Options
    • Command-Line “add-apps”
    • Command-Line “add-workflows”
  • GeneFlow Config File
  • Run Pre-Installed Workflows in the CDC Environment
  • Install and Run a GeneFlow Workflow from the Community Repo
• GeneFlow Definition Language
  • Metadata
  • Inputs
  • Parameters
  • Steps
  • Apps
  • Dynamic Templating
  • Map Reduce
• Creating GeneFlow Apps
  • GeneFlow App Config File
    • Metadata
    • Inputs and Parameters
    • App Output
    • App Execution Methods
    • Execution Blocks
    • Conditional Blocks
  • Generating a GeneFlow App
• GeneFlow Tutorials
  • Basic App: Hello World
    • Configure the Environment
    • Clone the GeneFlow App Template
    • Define the App
    • “Make” the App
    • Test the App
    • Update the App README
    • Commit the App to a Git Repo
    • Summary
  • One-Step Workflow: Hello World
    • Clone the GeneFlow Workflow Template
    • Configure the Workflow
    • Add Test Data
    • Update the Workflow README
    • Commit the Workflow to a Git Repo
    • Install the Workflow from a Git Repo
    • Test the Workflow
    • Summary
  • Basic Workflow and App Inputs
    • Modify the “Hello World!” App
    • Modify the “Hello World!” Workflow
    • Summary
  • Piped Execution in Apps
    • Modify the “Hello World!” App
    • Modify the “Hello World!” Workflow
    • Summary
  • Conditional Execution in Apps
    • Modify the “Hello World!” App
    • Modify the “Hello World!” Workflow
    • Summary
  • Multi-Step Workflow
    • The “wc” app
    • Hello World output is the wc input
    • Update the workflow.yaml file
    • Summary
  • Advanced Workflow and App Inputs
  • Branching Workflow
  • Executing Containers in Apps
    • Clone the GeneFlow App Template
    • Configure the App
    • Inputs and Parameters
    • App Execution Methods
    • “Make” the App
    • Test the App
    • Update your README.rst
    • Upload your app
    • Summary
  • Build a Container for an App
    • Singularity Requirement
    • A Container for RNA-Seq
    • Singularity Recipe
    • Base Container
    • Copy Files
    • Set Environmental Variables
    • Metadata
    • Install your software
    • Container as an Executable
    • Build your image
    • Working with your image
    • Summary
  • Tapis Workflow Installation and Execution