Input and Output Directories - DeepPhe/DeepPhe-Release GitHub Wiki

Running DeepPhe

There are a variety of ways to run the DeepPhe pipeline. Below we describe how to tell the system where to find the input and where to place output.

Using a GUI

The Piper File Submitter GUI can be launched from the command line or by using a maven profile.

Note these parameters within the GUI

  • Input Directory - point to the directory containing your files to be processed
  • Output Directory - point to the directory where output files and subdirectories will be created

Using a Command Line Tool

If you start DeepPhe by using the PiperFileRunner from cTAKES, the arguments to the -i and -o parameters are used for Input Directory and Output Directory.

For example, you might use these parameters

-p  
data/pipeline/DeepPhe.piper  
-i  
data/sample/reports/  
-o  
"/Temp/DeepPhe-output/run001"

where data/sample/reports/ contains a subdirectory for each patient to be processed.

Related pages

See Naming Input Files.

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