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Pipeline Runner GUI Configuration

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seanfinan edited this page Feb 16, 2022 · 2 revisions

Configuring the DeepPhe Pipeline Runner GUI

Welcome to the DeepPhe Pipeline Runner GUI

Before we run, we first need to configure the GUI to process the example patient reports. Set the parameters as follows:
(To change Input and Output directories you have to click the blue folder on the right end of the rows and select the file destination)
(To change Neo4jUri, Neo4jUser, or Neo4jPass you have to click the blank space and type in the Information)

  • InputDirectory: /Users/yourHomeDirectory/DeepPheDocs
  • OutputDirectory: /Users/yourHomeDirectory/DeepPheDocsOutput (directory must exist on filesystem)
  • StartNeo4j: (leave blank)
  • StopNeo4j: (leave blank)
  • Neo4jUri: bolt://127.0.0.1:7687
  • Neo4jUser: neo4j
  • Neo4jPass: neo4jpass

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Mission

Installation
   Windows
   Mac
   Linux
   Known Issues

Quickstart
   Windows Quickstart Tutorial
   Mac Quickstart Tutorial
   Command line-execution

Using DeepPhe-XN With Your Own Files
   Input File Requirements
   Configuring DeepPhe Phenotype Summarizer
   Specifying and Interpreting Outputs

Example Files Description
   Using DeepPhe-XN Visualizer
   Additional Output File Types
   Example File Data Specifics

About the DeepPhe Pipeline
   Pipeline Description

Code Modules

Licensing
Funding
Contact / Help

Wiki Conventions

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