knowengdev/spreadsheets_transformation repository overview

⁠KnowEnG's Spreadsheet Transformations mini-pipeline.

This is the Knowledge Engine for Genomics (KnowEnG), an NIH BD2K Center of Excellence, Spreadsheets Transformation.

Dockerfile on GitHub⁠

⁠Prerequisite: Install Docker⁠

Parameters based spreadsheet transformations with functionality: Subset Expression Based on Phenotype, Intersection, Subset Genes, Union, Group Then Apply a Function, Transpose, Numerical Transformation and Numerical Details.

This pipeline transforms a given spreadsheet, by one of nine basic methods that one can choose from:

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⁠How to run this pipeline's image with our data

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1. Install Docker - follow the instructions in this link. ============

Install Docker Engine⁠

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

docker pull knowengdev/spreadsheets_transformation:06_15_2018

1. Create a directory to hold the output data. ============

mkdir local_results

1. Start docker mounted with the full path to your output directory. =========== docker run -v /full/path/local_results:/home/test/run_dir -it knowengdev/spreadsheets_transformation:06_15_2018

2. At the new command prompt change to the test directory. =========== cd test

3. Set up the environment. ============= make env_setup

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1. Use one of the following "make" commands to select and run a transformation option: ===========

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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, in the local_results directory.

*** see the git hub directions *** Spreadsheet Transformations ReadMe on github⁠

1. Start docker in the directory with your your_custom_run_file.yml file. =========== docker run -v `pwd`:/home/test/run_dir -it knowengdev/spreadsheets_transformation: 06_15_2018

2. Change to the run directory (with your_custom_run_file.yml) and create a results directory. =========== cd ./test/run_dir mkdir results

3. Run with the options in your custom YAML file. ========= python3 ../../src/spreadsheets_transformation_pipelines.py -run_directory ./ -run_file your_custom_run_file.yml

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⁠============ How to run the jupyter notebooks with Docker.

(without installing jupyter on your computer)

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1. Copy and paste this line into a terminal window and hit enter. ========= docker run -p 8888:8888 knowengdev/spreadsheets_transformation:kubetest

2. Start your browser and paste this line into the URL window. ========= http://localhost:8888/

3. Copy the token and paste it into the login box. ========= http://localhost:8888/tree?token=9f4c0f8741405385271fb630f661580d1af86f031c54116d

(just this part) 9f4c0f8741405385271fb630f661580d1af86f031c54116d

1. Select the Spreadsheets_Transformation.ipynb and when it opens select Cell - Run All to start the notebook.

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