(support oneTBB) fatal error: tbb/mutex.h: No such file or directory

[thekswenson]

I'm using Ubuntu 22.04 and cannot compile Sibeliaz:

In file included from /.../software/SibeliaZ/TwoPaCo/src/graphdump/graphdump.cpp:17:
/.../software/SibeliaZ/TwoPaCo/src/graphdump/../common/streamfastaparser.h:8:10: fatal error: tbb/mutex.h: No such file or directory
    8 | #include <tbb/mutex.h>
      |          ^~~~~~~~~~~~~

The problem with with the TwoPaCo submodule and is related to this bug report: https://github.com/medvedevgroup/TwoPaCo/issues/28

If I'm reading that report correctly, the only way to us Sibeliaz would be to somehow apply a patch from the pufferfish repo. I that correct?

[thekswenson]

I replaced the TwoPaCo submodule with the code from the pufferfish repo. I then modified added to the CMakeLists.txt from this project:

find_package(TBB 2021.4
  COMPONENTS tbb tbbmalloc tbbmalloc_proxy
)

I removed the lines

add_dependencies(graphdump libtbb)
add_dependencies(twopaco libtbb)

from the pufferfish CMakeLists.txt that I had copied.

Now TwoPaCo compliles, but alas, the offending code also exists in the SibeliaZ source, so now I'm running into the same issue with that code!

[iminkin]

Hi @thekswenson ,

Can you use bioconda on your machine? That is probably the easiest way to install.

[thekswenson]

I forgot about that option. Thanks.