No, apptainer run does not automatically source ~/.bashrc like an interactive login shell would.

Key Behavior:

• apptainer run: Executes the %runscript in a non-interactive shell → .bashrc is not sourced.
• apptainer shell: Starts an interactive shell → .bashrc is sourced (if using Bash and the file exists in the container or mounted home).

Equivalent Solutions:

1. Explicitly source it in %runscript (for apptainer run):

   bash
   Copy
   # In your Singularity/Apptainer definition file:
   %runscript
   source ~/.bashrc && exec "$@"

2. Use BASH_ENV (for non-interactive Bash):

   bash
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   %environment
   export BASH_ENV=/path/to/your/bashrc

3. Switch to apptainer shell if you need an interactive environment with .bashrc loaded.

4. Mount and source manually:

   bash
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   apptainer run --bind ~/.bashrc:/root/.bashrc your_container.sif

   (Then ensure the runscript sources it.)

For most cases, option 1 or 2 is the cleanest equivalent.