@robqiao You should include an easyconfig for this dependency in this pull request (see failing tests in Travis), and use foss/2017a as toolchain rather than specifying the toolchain for the dependency, i.e.:

toolchain = {'name': 'foss', 'version': '2017a'}
...
dependencies = [
    ('HTSlib', '1.2.1'),
]

@boegel thanks. Is that a convention to use a tool chain option if any dependencies use one, even when parent itself not use any?

Since PileOMeth is also being compiled, it's a lot better to specify the toolchain to something that is not dummy, since then EasyBuild will also set up the build environment (stuff like $CC, $CFLAGS, etc.)

The dependencies by default will inherit the parent toolchain. You can hard specify to use a particular toolchain on a per-dependency basis, but then these should be a subtoolchain of the parent toolchain. In practice, we only do this when a particular dependency was installed with a dummy toolchain (e.g. a binary tool that doesn't require compiling).

See also http://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html#dependencies

@robqiao Any particular reason you are also copying the *.c and *.h files?

@boegel some of our users use .h to build their own functions using existing functions, but I guess I should remove these for this purpose. :)

Well, than you should only include the *.h files, and copy them to the include subdirectory (so that the location gets added to $CPATH)?

please use 'lib/libhts.%s' % SHLIB_EXT rather than hardcoding the .so

Thanks for the tip.