Shell Automation (`.bashrc`)

The “Automation Engine” for your SciServer container is a persistent .bashrc file. While containers have a default system configuration, any changes you make to the local ~/.bashrc are lost on restart.

To solve this, SciServer has been configured to automatically source a specific persistent .bashrc file from your User Storage on any new session.

How it Works

When you open a terminal or launch a JupyterLab session, the container runs this logic automatically:

if [ -f $HOME/workspace/Storage/$SCISERVER_USER_NAME/persistent/.bashrc ]; then
    . $HOME/workspace/Storage/$SCISERVER_USER_NAME/persistent/.bashrc
fi

Key Implications:

Automatic Loading: If you create this file in your persistent storage, it loads every time.
Precedence: Because it runs last, it overrides any default system aliases or variables.
Cross-Container: It persists across different images and container restarts.

Setting Up Your Automation Engine

1. Create the file

Create the file at the specific persistent location:

nvim $HOME/workspace/Storage/$SCISERVER_USER_NAME/persistent/.bashrc

2. Add Your Customizations

Here are sample uses for your persistent .bashrc.

A. Persistent Aliases

Save typing for long commands:

# Shortcut to activate your persistent mamba environment
alias myenv='mamba activate ~/workspace/Temporary/$SCISERVER_USER_NAME/scratch/envs/my-analysis'

# print "hello <username>" every time a new terminal is opened
alias sayhello='echo "hello $SCISERVER_USER_NAME"'

B. Environment Variables

Set default paths or API keys:

# Tell Python to look in your persistent storage for custom modules
export PYTHONPATH="$HOME/workspace/Temporary/$SCISERVER_USER_NAME/scratch/custom_libs:$PYTHONPATH"

C. Automation Recipes

As seen in the Persistent Python Environments and Persistent SSH and Terminal configs guides, you can use this file to automatically register kernels or link SSH keys.

Testing and Troubleshooting

Apply Changes Immediately

To test changes without restarting the container, run:

source $HOME/workspace/Storage/$SCISERVER_USER_NAME/persistent/.bashrc

Troubleshooting Errors

If your terminal starts behaving strangely (e.g., commands not found) after editing this file:

Disable it temporarily:

mv $HOME/workspace/Storage/$SCISERVER_USER_NAME/persistent/.bashrc $HOME/workspace/Storage/$SCISERVER_USER_NAME/persistent/.bashrc.bak

Restart your terminal.
Fix the syntax error in the .bak file and rename it back.

Shell Automation (.bashrc)