Using this package requires one of hmmer or diamond to be present

How are these accessed by eggnog-mapper? Are they just called as binaries, expecting them to be in PATH? If so, they should probably be pinned down to specific dependencies. There are a couple of ways of doing this - probably best to look at using makeWrapper (see https://nixos.org/nixpkgs/manual/#ssec-stdenv-functions) to force the PATH seen by the eggnog executable.

As for making them "optional" - you can make the arguments to the toplevel function "optional" by giving them a "default" of null - e.g. ..., diamond ? null, .... If you do this you'll probably want to use an assert statement to ensure they're not both null. Then where you're using these variables you'll be wanting to cope with the fact that either of them could be null.

At some point you'll have to make a decision though over which of them you'll want to be depended on by the "default" package that gets built by hydra.

Thanks for the feedback. For the moment, I think it's better to make both of them dependencies for the user's convenience.

I added makeWrapper arguments to ensure eggnog-mapper finds the right binaries.

Builds for me and binaries appear to trivially "work" on non-nixos linux x86_64.

I slightly wonder whether it would be "nicer" to reformat the names of the installed executables to something cleaner like download-eggnog-data rather than download_eggnog_data.py, but it's probably not important.

I slightly wonder whether it would be "nicer" to reformat the names of the installed executables to
something cleaner like download-eggnog-data rather than download_eggnog_data.py, but it's probably
not important.

Even if those are nicer, the current names are mentioned in the eggnog-mapper docs, so it would be confusing for the user.

Thanks. Rebased to master, squashed & re-pushed.