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The Tezos documentation all show the storage expression being defined inline when compiling storage. For example, using cameligo:

ligo compile storage src/counter.mligo 5 --entry-point main

If I try to put the expression '5' in a file, like initStorage.mligo, then using the file name instead, this does not seem to work.

Is it possible to define the initial storage in a file then compile storage with that file?

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You can use the standard shell command substitution operators ` ` or $():

ligo compile storage src/counter.mligo "$(cat initStorage.mligo)" --entry-point main

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