How can I compile gatb-core using Boost and hdf5 libraries installed separately, rather than those under thirdparty/? (This is needed to create a proper recipe for installing gatb with the bioconda package manager). Thanks for help!
Hi Ilya, the short answer is that you currently cannot as of today.
A GATB team member attempted to do that before, but this entails to modify gatb's CMakeLists.txt to find the system boost and hdf5 libs, as well as a few #include's. Currently the easiest solution is to ship (a subset of) boost and hdf5 along with gatb-core.
Thing is, we also modified hdf5's CMakeLists in some places (e.g. to allow compilation without zlib, to rename the produced h5dump binary, and apparently for static compilation), so going back to vanilla hdf5 will require some testing on our side.
Any obstacle towards allowing gatb-core package to contain parts of boost and hdf5?