From 8eb9f4a4dbeaf19825c1ade259ac10aab96563d6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= <berenice.batut@gmail.com>
Date: Wed, 6 Mar 2024 10:37:12 +0100
Subject: [PATCH] Use conda environment and Makefile

---
 Makefile        | 33 +++++++++++++++++++++++++++++++++
 README.md       | 24 ++++++++++++++++++++++++
 environment.yml |  7 +++++++
 3 files changed, 64 insertions(+)
 create mode 100644 Makefile
 create mode 100644 environment.yml

diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..137b879
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,33 @@
+# 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
diff --git a/README.md b/README.md
index fb82e9e..f2c3f7f 100644
--- a/README.md
+++ b/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)
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..ac1e687
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,7 @@
+name: microgalaxy_technical_paper
+channels:
+- conda-forge
+- defaults
+dependencies:
+- jupyter
+- pandas
\ No newline at end of file