problems installing and compiling STAR: make STARforMacStatic

[Stephen Chapman]

Hi all, I'm new to this, as you can probably tell. I thank you all for your patience.

I've downloaded STAR, pointed the directory to the source folder, then wanting to make STAR so (make STARforMacStatic CXX=/path_to_gcc) which for me is:

Stephens-MBP:source stephenchapman$ make STARforMacStatic CXX=/Library/Developer/CommandLineTools/usr/bin

The output i've received is:

/Library/Developer/CommandLineTools/usr/bin -c   -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 26 Sep 2017 09:36:23 BST :/Users/stephenchapman/Downloads/STAR-2.5.3a 3/source"' -D'COMPILE_FOR_MAC'  SharedMemory.cpp

make: /Library/Developer/CommandLineTools/usr/bin: Permission denied

Any idea why the permission has been denied and how I can rectify this?

I have checked that GCC is installed, as when I type:

Stephens-MBP:source stephenchapman$ gcc --version

I receive:

Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1

Apple LLVM version 8.0.0 (clang-800.0.42.1)

Target: x86_64-apple-darwin15.6.0

Thread model: posix

InstalledDir: /Library/Developer/CommandLineTools/usr/bin

So yep, back to the permission part if anyone can help me with this!

Cheers

Stephen

[Alexander Dobin]

Hi Stephen,

there should be g++ executable in the /Library/Developer/CommandLineTools/usr/bin/ directory, and you need to point CXX to it:

$ make STARforMacStatic CXX=/Library/Developer/CommandLineTools/usr/bin/g++

You can also try to use the compiled for Mac executable in the STAR distribution:

bin/MacOSX_x86_64/STAR

Cheers

Alex