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gmarcais / Jellyfish

A fast multi-threaded k-mer counter
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path to jellyfish includes #139

Closed rsharris closed 5 years ago

rsharris commented 5 years ago

I distribute a C++ package that links with the jellyfish library. I don't understand the proper way to access the .hpp files, as there seems to be an unusual extra layer in the path hierarchy.

After installing jellyfish, I find that the .h files are in ${HOME}/includes/jellyfish-2.2.10/jellyfish/*.hpp . For other packages, the paradigm is for installation to put them in ${HOME}/includes/some_package/*.hpp

If I add the usual -I${HOME}/includes to my compile command line, compilation (of MY package) fails at #include <jellyfish/mer_dna.hpp> because the path isn't right. I could make that <jellyfish-2.2.10 .jellyfish/mer_dna.hpp> and I assume that would work, but it seems like the wrong thing to do.

What I've been doing, after installation, is to make a symlink to hop past the jellyfish-2.2.10 level. This also seems like the wrong thing to do. Especially since anyone trying to build my package will also be expected to do that.

Nor do I really want to hardcode a jellyfish version number in my Makefile.

So my question is, what's the right way to do this?

gmarcais commented 5 years ago

The right way to do it is to use pkg-config. The installer should have created a file ${HOME}/lib/pkgconfig/jellyfish-2.0.pc with the proper path to compile against Jellyfish.

Do: export PKG_CONFIG_PATH=${HOME}/lib/pkgconfig.

Then add $(shell pkg-config --cflags jellyfish2.0) and $(shell pkg-config --libs jellyfish-2.0) in your CFLAGS and LIBS variable of your Makefile to get the proper flags. If you use autotools, pkgconfig is also directly supported.

Hope this helps.

rsharris commented 5 years ago

Cool, thanks!

mmokrejs commented 5 years ago

@gmarcais Shouldn't that be pkg-config --cflags-only-I jellyfish2.0? @kiwifb what would you say?

gmarcais commented 5 years ago

@mmokrejs Sure, maybe. The point is you should use pkg-config to get this information, as the information is the most correct one (created by the installer). Now, which switch or pkg-config you actually use for a given variable in your particular build system, that's up to you.

kiwifb commented 5 years ago

I am at a conf will look later.

kiwifb commented 5 years ago

Yes @mmokrejs that is right. At least if you only want the include file, --cflags may give you more stuff like macros (-D...) or specific flags (-pthread) if necessary. I would only consider --cflags-only-I for very specific usage like feeding a distutils toolchain in python.