microGalaxy 2025 Paper

This repository includes all the scripts written to produce figures in the paper along with the resulted figures

Requirements

• Install conda

  $ make install-conda
  

• Create the conda environment

  $ make create-env
  

Usage

Retrieve citations

• Launch Jupyter to access the notebooks to generate graphs

  $ make run-jupyter
  

• Go to http://localhost:8888 (a page should open automatically in your browser)

Update data

• Launch the dedicated script

  $ bash bin/get_data.sh
  

Rebuild Extended Figures

Rscript -e "rmarkdown::render('bin/citations-graphs.Rmd',output_file = tempfile())"     # Extended Figure 1
Rscript -e "rmarkdown::render('bin/survey-figure.Rmd', output_file = tempfile())"       # Extended Figure 2
Rscript -e "rmarkdown::render('bin/tools-graphs.Rmd', output_file = tempfile())"        # Extended Figure 3
Rscript -e "rmarkdown::render('bin/workflows-graphs.Rmd', output_file = tempfile())"    # Extended Figure 4
Rscript -e "rmarkdown::render('bin/tutorials-graphs.Rmd', output_file = tempfile())"    # Extended Figure 5