Fix MacOS support

[fabio-t]

It's almost done, but there's still some weirdness. Must try it in a few more macs.

[fabio-t]

Current issues: the following dependency formatting doesn't work for some (it worked for joseph, and in a clean virtual environment):

ngslib;platform_system=='Linux'

It either tries to compile it, and fails of course, or it crashes on pip setup.py egg_info. @jovesus can you paste the error message here?

[fabio-t]

Right now, if the user first installs python via Homebrew, there shouldn't be problems. Hopefully.

brew install python
pip install rgt --user

More testing needs to be done.

[fabio-t]

Pysam caused MacOS regressions in the last few versions. While waiting for the fix, we've had to block the pysam dependency to version 1.11.1.

For reference: pysam-developers/pysam#475

[fabio-t]

Triplexes is not compiled for Mac. @jovesus could you have a look at that (when you are back)?

[zjin1126]

SeqAn C++ template is not compatible with LLVM libc++, which used by clang in default settings.
Compile Triplexes with GNU libstdc++ can bypass this problem.

Build Triplexes without OpenMP:

SRC_ROOT=/path/to/triplexes

cmake $SRC_ROOT \
-DCMAKE_CXX_FLAGS="-stdlib=libstdc++" \
-DCMAKE_BUILD_TYPE=Release \
-DSHAREDLIBRARY=TRUE

make

Pre-installed clang on macOS doesn't support OpenMP, so install clang via Homebrew.
Build Triplexes with OpenMP:

brew install llvm # clang with openmp support

export CC=/usr/local/opt/llvm/bin/clang
export CXX=/usr/local/opt/llvm/bin/clang++

cmake $SRC_ROOT \
-DCMAKE_CXX_FLAGS="-I/usr/local/opt/llvm/include -stdlib=libstdc++" \
-DCMAKE_C_FLAGS="-I/usr/local/opt/llvm/include" \
-DCMAKE_SHARED_LINKER_FLAGS="-L/usr/local/opt/llvm/lib" \
-DOpenMP_C_FLAGS="-fopenmp" \
-DOpenMP_CXX_FLAGS="-fopenmp" \
-DCMAKE_BUILD_TYPE=Release \
-DSHAREDLIBRARY=TRUE

make

These cmake options can let rgt-TDF run on macOS.

After compile, copy libtriplexator.dylib to rgtdata/lib and modify path_triplexator in data.config to path_triplexator=$HOME/rgtdata/lib/libtriplexator.dylib.

[fabio-t]

@zjin1126 this is VERY helpful! Thanks. We will give this a try soon.

[chaochungkuo]

@zjin1126 Thank you for your contribution. Last week I tried to install openMP on mac and use llvm to compile, but because of not having sufficient understanding of cmake, I couldn't work it out. Your comment solves our problem exactly. Thank you.

Now if RGT is successfully installed on Mac, it works as nrmal as on Linux.

[fabio-t]

I'm fairly sure now RGT works fine on Mac. We'll open specific issues in the future, in case of need.