To avoid having to specify --color=always every time you run ls inside an Apptainer container on Red Hat Linux 9, you can set the LS_COLORS environment variable or create an alias for ls inside the container. However, since you want a solution that does not affect other commands and is specific to ls, the best approach is to:

1. Use an Apptainer Run Script

Create a run script for your container that automatically sets the --color=always flag for ls without affecting other commands.

Steps:

1. Create a run script (e.g., %runscript in your .def file or a custom script).
2. Override the ls command to always include --color=always.

Example:

If you're building a container from a definition file (mycontainer.def), add:

bash
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%runscript
export LS_COLORS="always"
alias ls="ls --color=always"
exec "$@"

Then rebuild the container:

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apptainer build mycontainer.sif mycontainer.def

Alternative (for existing containers):

If you don't want to rebuild, you can bind a custom wrapper script for ls:

1. Create a script (e.g., /tmp/ls_wrapper.sh):

   bash
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   #!/bin/bash
   ls --color=always "$@"

2. Make it executable:

   bash
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   chmod +x /tmp/ls_wrapper.sh

3. Run the container with the wrapper script as the ls command:

   bash
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   apptainer exec --bind /tmp/ls_wrapper.sh:/usr/local/bin/ls mycontainer.sif ls

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2. Use a Shell Configuration File (Inside the Container)

If you have control over the container's filesystem, you can modify the shell configuration (e.g., .bashrc) to alias ls:

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echo 'alias ls="ls --color=always"' >> ~/.bashrc

But this affects all users and shells inside the container.

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3. Use SINGULARITYENV_LS_COLORS (Environment Variable)

If you want to enforce color only for ls without modifying the container, you can pass the environment variable when running Apptainer:

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apptainer exec -e LS_COLORS=always mycontainer.sif ls

But this still requires specifying it each time.

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Best Solution for Your Case

Since you want a persistent, ls-only solution, the run script or wrapper script approach is the cleanest. If you want to avoid rebuilding the container, the wrapper script method is the most flexible.

Would you like help implementing one of these approaches?