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broadinstitute
Add OS X testing on travis
It looks like it is now generally available and default: travis-ci/travis-ci#2320
Just tracking a note here on where we're at currently. It seems like almost everything works on OSX with the exception of three tools: VPhaser2, Kraken, Diamond.
- Kraken and Diamond don't even have bioconda builds for OSX, which seems weird, but ought to be addressed upstream of here in bioconda.
- VPhaser2 is on us, and I'm not totally sure if it ever worked on OSX... problems with dynamically linked libgomp.
Encouraging to know that everything else actually seems to work though (py.test test/unit and test/integration only fails on the above three tools).
I'm pretty sure I mentioned to @tomkinsc at some point that the OS X trinity builds don't work. I have an OS X trinity on my conda channel but it is only the latest version.
I'm actually not sure why kraken doesn't have a build. Diamond doesn't have a build because of libc++/libstdc+++ incompatibilities between the anaconda channel boost build. Either way - it's unlikely that an OS X machine has that much memory to run either realistically.
An OSX machine should definitely have enough memory given a small enough db, (like minikraken and all our Travis unit test dbs). Plus Diamond is useful for other things (blast-like functionality) other than metagenomics... shouldn't assume the tool isn't useful just cause it can't load the big db..