Use conda environment and Makefile

Makefile

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+# Settings
+CONDA_ENV=microgalaxy_technical_paper
+SHELL=bash
+
+CONDA=$(shell which conda)
+ifeq ($(CONDA),)
+	CONDA=${HOME}/miniconda3/bin/conda
+endif
+
+default: help
+
+install-conda: ## install Miniconda
+	curl -L $(MINICONDA_URL) -o miniconda.sh
+	bash miniconda.sh -b
+.PHONY: install-conda
+
+create-env: ## create conda environment
+	if ${CONDA} env list | grep '^${CONDA_ENV}'; then \
+	    ${CONDA} env update -f environment.yml; \
+	else \
+	    ${CONDA} env create -f environment.yml; \
+	fi
+.PHONY: create-env
+
+ACTIVATE_ENV = source $(shell dirname $(dir $(CONDA)))/bin/activate $(CONDA_ENV)
+
+run-jupyter: ## run jupyter notebooks
+	$(ACTIVATE_ENV) && \
+		jupyter notebook
+
+help:
+	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
+.PHONY: help

README.md

@@ -1,3 +1,27 @@
 # microGalaxy Technical Paper 2024 Preparation
 
 This repository includes all the scripts written to produce figures in the paper along with the resulted figures
+
+# Requirements
+
+- Install [conda](https://conda.io/miniconda.html)
+
+    ```
+    $ make install-conda
+    ```
+
+- Create the conda environment
+
+    ```
+    $ make create-env
+    ```
+
+# Usage
+
+- Launch [Jupyter](https://jupyter.org/) to access the notebooks to generate graphs
+
+    ```
+    $ make run-jupyter
+    ```
+
+- Go to [http://localhost:8888](http://localhost:8888) (a page should open automatically in your browser)

environment.yml

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+name: microgalaxy_technical_paper
+channels:
+- conda-forge
+- defaults
+dependencies:
+- jupyter
+- pandas