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.
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://github.com/dlanier/knoweng_transform.git
- (depreciated and removed) https_NOT//github.com/dlanier/knoweng_dev_tools.git
Production repositories included: