Public Repository

Last pushed: 8 months ago
Short Description
This allows running KnowEnG pipelines and transformations in a docker container.
Full Description

Jupyter notebook research examples for transforming data files and running the pipelines


Note: Some example notebooks fail with incorrect port | password for the gene name database called by data cleanup.

First Install Docker - follow the instructions in this link.

Install Docker Engine

How to run this container from the command line.

pull the image:

docker pull knowengdev/jupyter_notebooks:08_18_2017

create a directory "user_data" (with your data) in the directory where you will run the container:

docker run -v `pwd`:/home/jovyan/work -it --rm -p 8888:8888 knowengdev/jupyter_notebooks:08_18_2017

In the terminal window copy the one time connection token to a browser URL window to run the notebooks
Note: the repositories named below will be left in the directory where you run this command
Output will be saved in "user_data/results" after the container is stopped
(or knoweng_dev_tools/test/ if developer tools is run)

The browser window will display jupyter mounted directories - change directory to run the notebook:

  • select: knoweng_transform
  • select: run_transform
  • click on the transformation notebook: Data_File_Transformations.ipynb

The browser will show that the notebook is not trusted so the cells must be run manually after selecting "Trust":

  • in the "Cell" menu select Run All
  • the list boxes and action buttons will appear below the directions for each transformation

Development repositories included but no longer on github:

  • (depreciated and removed) http_NOT://
  • (depreciated and removed) https_NOT//

Production repositories included:

Docker Pull Command