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I am trying to compile the genome assembler platanus 1.2.4 on Mac OSX Big Sur and run into several errors. Our lab has a high-powered mac that we would really like to use for genome assembly. I have also tried on OSX Catalina and with platanus-allee v2.2.2 and get the same errors.

(base) XXXX Platanus_v1.2.4 % make
g++ -o main.o -c main.cpp -std=c++0x -O3 -funroll-loops -Wall -fopenmp -finline-limit-50000 -lm -Dnullptr=0
clang: error: unknown argument: '-finline-limit-50000'
clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument]
clang: error: unsupported option '-fopenmp'
make: *** [Makefile:14: main.o] Error 1

I was able to get rid of the 3rd error (unsupported option '-fopenmp') with the homebrew llvm package to use OpenMP. I changed the compiler in the first line and added the -I/usr/local/opt/llvm/include to the second line (from this post)

CXX = /usr/local/opt/llvm/bin/clang
CXXFLAGS = -I/usr/local/opt/llvm/include -std=c++0x -O3 -funroll-loops -Wall -fopenmp -finline-limit-50000 -lm -Dnullptr=0

However, I can't figure out how to get through the '-finline-limit' and 'lm' errors. Has anyone dealt with these errors?

Thanks for your help!

user17185345
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1 Answers1

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The solution I found to this is use Docker to install an Ubuntu container.

I just set up the Ubuntu container, I installed build-essential, git-all, wget, nano, miniconda3, and with conda installed minimap2. After that the Platanus precompiled binary works perfectly inside it! Super easy!

Make sure to increase the memory, disk space, and cpu allowance for Docker so that it matches whatever you need for Platanus.

Ali Briceño
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user17185345
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