vladkim/ipynb repository overview

⁠Description

Base image for Docker images hosting documents in Jupyter notebook format. The layers of the image are as follows:

• Ubuntu 14.04 (base)
• r-base, r-base-dev, r-recommended
• ipython-3.2.1 and dependencies
• R kernel for ipython
• includes wget among other utilities

⁠How to Create a Derivative Docker Image

1. To create a docker image hosting software documentation in Jupyter notebook format, start your Dockerfile with the following line

FROM vladkim/ipynb:latest

1. Next, install all the R packages required for running your Jupyter notebook. You can provide an R script, which contains install commands for required R packages e.g.

RUN wget http://www.example.com/your_packages.R && \
     R < your_packages.R --no-save

This will download the hypothetical R script your_packages.R from www.example.com⁠ and pass the script to R with --no-save flag. 3. Finally add your .ipynb document, e.g. with COPY command:

COPY your_vignette.ipynb ./

⁠Further Links

• RNA-Seq workflow: gene-level exploratory analysis and differential expression⁠