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I'm trying to build Bitcoin Core and, if I understand it correctly, the configure script uses the --prefix= option twice, once for the inclusion of the depends build (from depends/README.md):

**Bitcoin Core's configure script by default will ignore the depends output.** In
order for it to pick up libraries, tools, and settings from the depends build,
you must point it at the appropriate `--prefix` directory generated by the
build. In the above example, a prefix dir named x86_64-w64-mingw32 will be
created. To use it for Bitcoin:

    ./configure --prefix=$PWD/depends/x86_64-w64-mingw32

And another usage of --prefix as it's usually used in configure, to specify a nonstandard install location (output from ./configure --help):

By default, `make install' will install all the files in
`/usr/local/bin', `/usr/local/lib' etc.  You can specify
an installation prefix other than `/usr/local' using `--prefix',
for instance `--prefix=$HOME'.

How can I specify an installation path and a depends path at the same time?

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You cannot set the installation path with ./configure, but only when running make install. You need to specify --prefix=once for ./configure and once for make install.

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