Update setup_env.sh

setup_env.sh

@@ -1,6 +1,29 @@
-#!/bin/bash
+#! /bin/bash
 
-conda env create -n bootcamp -f env.yml # runtime: ~13min
-~/.conda/envs/bootcamp/bin/python3 -m ipykernel install --user --name=python_bootcamp --display-name="Python 3 (bootcamp)"
-Rscript -e 'IRkernel::installspec(name="R_bootcamp", displayname="R (bootcamp)")'
+set -eu
 
+if [ ! -e "$HOME/Miniforge3-Linux-x86_64.sh" ]; then
+    wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -P $HOME
+fi
+
+if [ ! -e "$HOME/miniforge3" ]; then
+    bash $HOME/Miniforge3-Linux-x86_64.sh -b
+fi
+
+export PATH="$HOME/miniforge3/bin:$PATH"
+
+mamba env create -f env.yml -y
+mamba run -n bootcamp ipython kernel install --user --name=python_bootcamp --display-name="Python 3 (bootcamp)"
+mamba run -n bootcamp Rscript -e 'IRkernel::installspec(name="R_bootcamp", displayname="R (bootcamp)")'
+
+mamba init
+source ~/.bashrc
+
+touch ~/.bash_profile
+cat >> ~/.bash_profile << EOF
+if [ -f ~/.bashrc ]; then
+        . ~/.bashrc
+fi
+EOF
+
+rm ~/Miniforge3-Linux-x86_64.sh