I'm trying to install a bioinformatics tool, called Daccord on my Mac.

Unfortunately my computer savvy is very limited and my troubleshooting is pretty much trial and error.

The README says:

daccord needs libmaus2 https://github.com/gt1/libmaus2. libmaus2 needs to be built with support for the GMP library. When libmaus2 is installed in ${LIBMAUSPREFIX} then daccord can be compiled and installed in ${HOME}/daccord using

autoreconf -i -f
./configure --with-libmaus2=${LIBMAUSPREFIX} \
make install

I did install libmaus2 (at least I hope I did), I also installed GMP, but I have no idea whether libmaus2 was "built with support for the GMP library".

My guess is that I have to replace ${LIBMAUSPREFIX} with the right path? Maybe ${HOME} too.

I tried /usr/local/bin because the libmaus-README said:

By default, make install installs the package's commands under /usr/local/bin, include files under /usr/local/include, etc.

I also tried the path of the libmaus release file.

So far the result is always:

configure: error: Package requirements (libmaus2 >= 2.0.352) were not met:
No package 'libmaus2' found
Consider adjusting the PKG_CONFIG_PATH environment variable if you
installed software in a non-standard prefix.

Alternatively, you may set the environment variables libmaus2_CFLAGS
and libmaus2_LIBS to avoid the need to call pkg-config.
See the pkg-config man page for more details.

Now, I additionally tried to set the PKG_CONFIG_PATH using

export PKG_CONFIG_PATH=/usr/local/lib

/usr/local/lib contains libmaus2 and a lot of other files starting with libmaus2 so I would guess that's the right path. But

./configure --with-libmaus2=/usr/local/lib --prefix=${HOME}/daccord


./configure --with-libmaus2=${LIBMAUSPREFIX} --prefix=${HOME}/daccord

Still results in the error mentioned above.

Would be great if someone could give me a few pointers as to how to proceed.

  • Could you indicate the path where your libmaus2 is located and the PKG_CONFIG_PATH environment variable. – harrymc Sep 23 '18 at 17:38
  • libmaus seems to be in /usr/local/lib. I just now changed the PKG_CONFIG_PATH to /usr/local/lib. echo $PKG_CONFIG_PATH now results in /usr/local/lib. ./configure --with-libmaus2=${LIBMAUSPREFIX} --prefix=${HOME}/daccord or ./configure --with-libmaus2=/usr/local/lib --prefix=${HOME}/daccord both still result in "No package 'libmaus2' found". – BlindKungFuMaster Sep 24 '18 at 13:44

It seems to me that libmaus2 was not correctly installed, so you might need to really install it after all.

I'm not a user of libmaus2, but I did notice that it says that you need to provide the libmaus2 base directory when calling configure for a dependent.

Meaning that if you configured libmaus2 with :

./configure --prefix=${HOME}/libmaus2

then you might use for building the dependent package :

./configure --with-libmaus2=${HOME}/libmaus2

I also have no idea whether libmaus2 is built by default with support for the GMP library, but this might be a config parameter that you can check.

EDIT: Daccord is finally running after some help from the author. Here is how:

First, gmp had to be given the libmaus2 path:

./configure --prefix=/usr/local
make install

Then libmaus2 had to be informed about that too:

./configure --with-gmp=/usr/local --prefix=/usr/local
make install

Then daccord could be installed with:

./configure --with-libmaus2=/usr/local --prefix=${HOME}/daccord
make install

And, all that has to be done with the newest release version of both libmaus2 and daccord, which are not hosted on github, but on gitlab.

  • As I said, I'm not a user of libmaus2. If this answer doesn't help you advance, let me know and I'll delete it. – harrymc Sep 24 '18 at 14:03
  • Ah, well, first of all, thank you for your answer. I contacted the author and made some progress, but it doesn't run yet. I think you deserve the bounty for at least trying to help me out. I will probably edit your answer once I know the actual solution, if that's ok with you. – BlindKungFuMaster Sep 30 '18 at 5:46
  • @BlindKungFuMaster: Which bounty ? – harrymc Oct 1 '18 at 20:01
  • Did you not get it? I guess I had to accept the answer? I thought if there is only one answer it'll go to that one. I guess I'll bounty some more. – BlindKungFuMaster Oct 1 '18 at 20:44
  • Ok, further bounties don't work because apparently bounties need to double every time and I'm 37 rep short of that right now. So sorry, seems like I wasted your time and my rep. – BlindKungFuMaster Oct 1 '18 at 20:51

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