Canu installation, error with GCC compiler

Question

[dicenhour]

I am trying to install canu-2.0 on my computer but when I try to build it I keep getting the following error:

Canu cannot be compiled with this compiler. Please install GCC and/or specify a non-Clang compiler on the command line, e.g., make CC=/path/to/gcc CXX=/path/to/g++

I previously installed gcc but I'm not sure what to do here. I followed the author's install instructions, trying both ways the suggested:

To install from a binary distribution (recommended installation method): tar -xJf canu-2.0.*.tar.xz

To install from source code (the file can be named either canu-v2.0.tar.gz or just v2.0.tar.gz, depending on how it is downloaded): gunzip -dc canu-v2.0.tar.gz | tar -xf - cd canu-2.0/src make -j 8 cd ..

I receive this error when I use the command make -j 8. Any help on how to proceed would be greatly appreciated. Thank you.

[Arup Ghosh]

Use conda to avoid dependency related issues.

https://anaconda.org/bioconda/canu

[GenoMax]

If you downloaded binary i.e. compiled canu then you don't need to do anything else. Just uncompress the file as noted above and run. For macOS you would need to get Darwin file. If you are running masOS catalina then check to see if this binary will run. No 32-bit software runs on Catalina.

Answer 1

[Mensur Dlakic]

make CC=/path/to/gcc CXX=/path/to/g++

You already have a recipe, so just add the ingredients. Assuming that your GCC installation was successful, in the make command above replace /path/to/gcc with the output of which gcc, and /path/to/g++ with the output of which g++.

On my computer, typing which gcc responds with /usr/bin/gcc and which g++ responds with /usr/bin/g++. Therefore, the make command would be:

make -j8 CC=/usr/bin/gcc CXX=/usr/bin/g++

[dicenhour]

Awesome, that worked! Thank you. I had tried that before but put the -j 8 at the end instead of the beginning.