Issue with Clang Compiler and gcc for MAJIQ pipeline installation

I was trying to install a splicing program "MAJIQ". I was able to run it on Centos but unable to install on MAC OS.

Description of the MAJIQ program.

Before installationMAJIQ installation requires the following lib/software to be installed in your system.

C++11 compiler with openMP. GCC includes that by default, but clang can be updated to include those (Clang/OMP). MAJIQ/VOILA has been tested to work with GNU GCC>=7.2, RedHat GCC>=4.7.2.HTSlib library. This is a C library for reading/writing high-throughput sequencing data developed by Samtools organisation. MAJIQ installation assumes the library and its header files are present in the Unix default locations (/usr/local/lib, /usr/local/include). If that is not the case the appropiate locations can be specified setting the following environment variables.

$ export HTSLIB_LIBRARY_DIR=/path/to/htslib/lib$ export HTSLIB_INCLUDE_DIR=/path/to/htslib/include

InstallationTo download and install MAJIQ/Voila run the following commands:

$ python3 -m venv env$ source env/bin/activate$ pip install pip -U$ pip install wheel setuptools -U$ pip install cython numpy GitPython -U $ pip install git+https://bitbucket.org/biociphers/majiq_stable.git#egg=majiq

If there is an error during install please verify that you're installing these packages with python 3 and the installed version of pip is current. Also, check if you have git, a c compiler (gcc, clang, etc.), and zlib installed.

Troubleshooting

1) I have tried conda install llvm, conda install gcc or conda install libgcc from https://github.com/velocyto-team/velocyto.py/issues/53

2) Also, tried in given way.

brew install llvmLDFLAGS="-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib"echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"'>> ~/.bash_profileexport LDFLAGS="-L/usr/local/opt/llvm/lib"export CPPFLAGS="-I/usr/local/opt/llvm/include"

Error in output

In file included from /private/var/root/env/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:    /private/var/root/env/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with ""#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]    #warning "Using deprecated NumPy API, disable it with " \     ^    1 warning generated.    g++ -bundle -undefined dynamic_lookup -arch x86_64 -g build/temp.macosx-10.9-x86_64-3.7/majiq/src/polyfitnb.o -o build/lib/majiq/src/polyfitnb.cpython-37m-darwin.so    building 'majiq.src.build' extension    creating build/temp.macosx-10.9-x86_64-3.7/majiq/src/internals    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I./majiq/src/internals -I./voila/c -Imajiq/src/internals -Ivoila/c -I/private/var/root/env/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/private/var/root/env/include -I/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c majiq/src/build.cpp -o build/temp.macosx-10.9-x86_64-3.7/majiq/src/build.o -fopenmp -DSCYTHE_COMPILE_DIRECT -DSCYTHE_PTHREAD    clang: error: unsupported option '-fopenmp'    error: command 'gcc' failed with exit status 1    ----------------------------------------ERROR: Command "/private/var/root/env/bin/python3 -u -c 'import setuptools, tokenize;__file__='"'"'/private/tmp/pip-install-8vjv35m9/majiq/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/tmp/pip-record-sfcn1usm/install-record.txt --single-version-externally-managed --compile --install-headers /private/var/root/env/include/site/python3.7/majiq" failed with error code 1 in /private/tmp/pip-install-8vjv35m9/majiq/