knowengdev/phenotype_prediction_pipeline repository overview

⁠KnowEnG's Phenotype Prediction Pipeline

This is the Knowledge Regression for Genomics (KnowEnG), an NIH BD2K Center of Excellence, Phenotype Prediction Pipeline that will be used to infer an 'omic'-drug association.

The user will need to do of the following in order for the system to learn how to predict the phenotype through regression:

• User must submit an ‘omic’ spreadsheet with samples as columns and genes as rows.
• User will also need to submit a phenotype value for each sample.

This will allow one to:

• Identify the best drug for a patient.

Given an omic spreadsheet of a collection of genes as well as the supplied phenotype value, the user will need to choose one of these options:

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⁠How to run this pipeline with our data

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⁠1. Install Docker - follow the instructions in this link

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Install Docker Engine⁠

⁠2. Get the current Docker Image. On the command line with internet connection:

============ docker pull knowengdev/phenotype_prediction_pipeline:08_01_2017

⁠3. Create or change to a directory to hold the output data.

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mkdir local_results and / or cd local_results

⁠4. Start the docker image connected to the (local_results) directory.

=========== docker run -v pwd:/home/test/run_dir/ -it knowengdev/phenotype_prediction_pipeline:08_01_2017

⁠5. At the docker image command prompt change to the test directory.

=========== .../home# cd test

⁠6. Set up the environment.

============= .../home/test# make env_setup

⁠7. Use one of the following "make" commands to select and run either of the following:

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⁠How to run this pipeline with Your data.

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*** Perform steps 1-3 as described above and use the local_results directory ***

⁠Create a custom YAML file, move that and your spreadsheet to the local_results directory

*** see the git hub directions *** Phenotype Prediction ReadMe on github⁠

*** make sure file named by YAML key "spreadsheet_name:" is in your local_results directory *** *** the path-names inside docker depend on the way you "mount" the run directory in step 4 *** *** therefore you may have to change the YAML path's to ../../ instead of ../ *** *** make sure your custom YAML file is in the local_results directory ***

1. Start docker with the container connected to your (local_results) directory. =========== docker run -v local_results:/home/test/run_dir -it knowengdev/phenotype_prediction_pipeline:06_02_2017

2. Change to the directory mounted in step 4. =========== .../home# cd ./test/run_dir .../home/test/run_dir# ls

*** the files in the local_results directory will be visible in this directory ***

1. Run Samples Clustering with the options in your custom YAML file. ========= python3 ../../src/phenotype_prediction.py -run_directory ./ -run_file your_custom_run_file.yml

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⁠Description of "run_parameters" file

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spreadsheet_name = features_train_clean.df
response_name = response_train_clean.df
test_spreadsheet_name = features_test_clean.df

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⁠Description of Output files are saved in results directory

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