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gtDMMB / gtfold

GTfold is a fast, scalable multicore code for predicting RNA secondary structure and is one to two orders of magnitude faster than the de facto standard programs and achieves comparable accuracy of prediction.
http://gtfold.sourceforge.net/
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Clarify dependencies #1

Open ceheitsch opened 3 years ago

ceheitsch commented 3 years ago

Have libomp (11.0.1) installed and cmake (3.19.4). Cmake is being treated "as a formula". There's no GUI here, so doesn't seem to be a need for a cask. If it matters, please clarify.

llvm (11.0.1) is also now installed. However, there were several caveats:

To use the bundled libc++ please add the following LDFLAGS: LDFLAGS="-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib"

llvm is keg-only, which means it was not symlinked into /usr/local, because macOS already provides this software and installing another version in parallel can cause all kinds of trouble.

If you need to have llvm first in your PATH, run: echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> ~/.profile

For compilers to find llvm you may need to set: export LDFLAGS="-L/usr/local/opt/llvm/lib" export CPPFLAGS="-I/usr/local/opt/llvm/include"

Please clarify which of these need to be addressed.

ceheitsch commented 3 years ago

I followed the "If you need..." directions and also the "For compilers...", but there's still some issue; see attached command line output. output.txt