set up conda and jupyter environment in home dir, not /tmp

Author: andrewdelman

Cloud_Setup/jupyter_env_setup.sh

@@ -29,29 +29,22 @@ echo -e "${red_start}Installed wget${nocolor_start}"
 sudo dnf install tmux -y
 echo -e "${red_start}Installed tmux${nocolor_start}"
 
-# retrieve and install miniforge in /tmp/
-# assuming EBS volume is already attached to instance
+# retrieve and install miniforge
 echo -e "${red_start}Starting Miniforge3 installation${nocolor_start}"
 mkdir -p /tmp
 wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" -O /tmp/Miniforge3.sh
-bash /tmp/Miniforge3.sh -b -p /tmp/conda
+bash /tmp/Miniforge3.sh -b -p ~/conda
 rm -f /tmp/Miniforge.sh
-source "/tmp/conda/etc/profile.d/conda.sh"
-source "/tmp/conda/etc/profile.d/mamba.sh"
+source ~/conda/bin/activate
 
 echo -e "${red_start}Completed Miniforge3 installation${nocolor_start}"
 
 # add conda and mamba to path
 mamba init
 
-# set paths to environment and package directories
-printf '\n# set conda environment and package directories' >> ~/.bashrc
-printf '\nexport CONDA_ENVS_PATH=/tmp/conda/envs' >> ~/.bashrc
-printf '\nexport CONDA_PKGS_DIRS=/tmp/conda/pkgs' >> ~/.bashrc
-source ~/.bashrc
+# # set paths to environment and package directories
 
-# create jupyter environment under /tmp/conda/envs/
-# (in EBS storage to save space in home directory)
+# create jupyter environment
 mamba create --name jupyter python=3.11 -y
 echo -e "${red_start}Created jupyter environment${nocolor_start}"
 

Cloud_Setup/jupyter_lab_start.sh

@@ -7,7 +7,7 @@ red_start='\033[0;31m'
 blue_start='\033[0;34m'
 nocolor_start='\033[0m'
 
-source /tmp/conda/bin/activate
+source ~/conda/bin/activate
 conda activate jupyter
 
 # Start configuration for Jupyter lab
@@ -20,7 +20,7 @@ jlab_start="jupyter Space lab Space --no-browser Space --autoreload Space --port
 tmux new -d -s jupyterlab
 
 # Execute commands in tmux window using send-keys
-tmux send-keys -t jupyterlab source Space /tmp/conda/bin/activate Enter
+tmux send-keys -t jupyterlab source Space ~/conda/bin/activate Enter
 tmux send-keys -t jupyterlab conda Space activate Space jupyter Enter
 tmux send-keys -t jupyterlab ${jlab_start} Enter