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Docker image for Bgee gene expression calls paper

Docker image containing all the packages necessary to generate the figures from "Robust Data-driven gene expression inference for RNA-seq using curated intergenic regions"

Build

docker build -t bgee-calls .

Interactive shell

docker run --rm -it -v "$PWD":/workspace -w /workspace bgee-calls bash

Jupyter Lab to explore notebooks step by step

docker run --rm -it -p 8888:8888 -v "$PWD":/workspace -w /workspace/notebooks bgee-calls \
  jupyter lab --ip=0.0.0.0 --no-browser --ServerApp.token='' --ServerApp.password=''

Execute all notebooks to generate all figrues and all files

docker run --rm -it -v "$PWD":/workspace -w /workspace/notebooks bgee-calls \
  bash -lc 'for nb in *.ipynb; do jupyter nbconvert --to notebook --execute --inplace "$nb"; done'

Execute only one notebook

docker run --rm -it -v "$PWD":/workspace -w /workspace/notebooks bgee-calls \
  jupyter nbconvert --to notebook --execute --inplace Figure1.ipynb