ERROR Performing build step for 'boost-libs'

Question

[Alessio]

Hi, I use a mac (Catalina) and when I try to install the breakdancer while running make the error appears [9%] Performing build step for 'boost-libs'. How can i fix this problem?

This is the code that I used to try to do the installation

git clone --recursive https://github.com/genome/breakdancer.git
cd breakdancer
mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local
make

ERROR

[  9%] Performing build step for 'boost-libs'
make[2]: *** [vendor/src/boost-libs-stamp/boost-libs-build] Error 1
make[1]: *** [CMakeFiles/boost-libs.dir/all] Error 2
make: *** [all] Error 2

[ATpoint]

Can you confirm that all requirements are fulfilled? https://github.com/genome/breakdancer/blob/master/INSTALL.md

There is also a conda version that might be of interest for easy installation, e.g. via miniconda. Also there are many alternative SV callers that are not archived by the power yet, maybe consider to simply use something else?

Answer 1

[ATpoint]

There is a python error at the beginning of the log complaining about syntax, this is most likely because the tool expects python2 but you have python3. I assume that in your /usr/bin there is still the default python2 executable. Therefore, try to set the PATH to have this directory to be checked first (and therefore use python from there`:

export PATH=/usr/bin/:$PATH

Don't put this in your .bash_profile though, simply type it into the Terminal when you compile the tool so it is not permanent, and then try compiling again.

On my Mac (10.14) it worked that way having cmake and boost installed, but it failed when having python3 as the default in PATH. It might be necessary to export this PATH everytime you use the tool, I do not know. Maybe a virtual environment or a script setting PATHs properly when you run it might help.

[Alessio]

I tried. but it generates me a new report with the same error.

Answer 2

[ATpoint]

I would simply install the miniconda package manager and then use conda install -c bioconda breakdancer.

[Alessio]

Thanks. It works!!!!