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I'm trying to create a simpler alias to launch MIT-scheme from the Terminal so I did:

alias mit-scheme="/Applications/MIT-Scheme.app/Contents/Resources/mit-scheme"

Then I can launch MIT-scheme by simply typing mit-scheme.

However if I close this Terminal window and open a new one, when I type mit-scheme I get -bash: mit-scheme: command not found.

What am I doing wrong?

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Running the command will define it for the current shell, but that's it. There's nothing specific about macOS here — this is a bash thing. You have to run the command on every shell. To do this automatically, add the line to a sourced file such as ~/.bash_profile.

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