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User Guide

Table of Contents

  1. Introduction
  2. Installation
    1. Requirements
    2. Downloading
    3. Setup and launching
  3. Interface overview
    1. Server library
    2. Personal library
    3. Workflow area
    4. Connection manager
    5. Provenance editor
    6. Preferences
    7. Search feature
    8. Checking for latest updates
    9. Running from the command line
  4. Building a workflow
    1. Dragging in modules
    2. Connecting modules
      1. Smartline
    3. Setting parameter values
    4. Data sources and sinks
    5. Remote file browser
    6. Processing multiple inputs
    7. Enable/Disable parameters
    8. Annotations
    9. Variables
    10. IDA
    11. Server changer
    12. Grammar view
  5. Execution
    1. Validation
    2. Executing a workflow
    3. Client Disconnect/Reconnect
    4. Server status
    5. Stopping a workflow
    6. Module statuses
    7. Viewing output
    8. Debugging execution
    9. Report a Bug
  6. Creating modules
    1. Simple modules
      1. Module tab
        1. General module information
        2. Citation information
      2. Parameters tab
        1. Executable location
        2. Maximum memory for SGE
        3. General parameter information
        4. Parameter types
        5. User defined filetypes
        6. Parameter arguments size
        7. Advanced parameter information
          1. Select dependencies
          2. Transformations
    2. Module groups
  7. Advanced Topics
    1. Syncing Execution Flow
    2. Exporting Pipeline Workflow to Script