From 1e3c575b7e32e762d4770b66585efc7215ccd0c8 Mon Sep 17 00:00:00 2001
From: David Laub <60826163+d-laub@users.noreply.github.com>
Date: Mon, 9 Sep 2024 17:31:41 -0700
Subject: [PATCH] Update setup_env.sh

---
 setup_env.sh | 31 +++++++++++++++++++++++++++----
 1 file changed, 27 insertions(+), 4 deletions(-)

diff --git a/setup_env.sh b/setup_env.sh
index 11e6d83..bb41046 100644
--- a/setup_env.sh
+++ b/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