Make Errors

[iPsychonaut]

I have attempted to build the repo but have been met with other errors mentioned above, and am currently facing this error:

make[2]: [CMakeFiles/hypo.dir/build.make:104: CMakeFiles/hypo.dir/src/Hypo.cpp.o] Error 1 make[1]: [CMakeFiles/Makefile2:561: CMakeFiles/hypo.dir/all] Error 2 make: *** [Makefile:156: all] Error 2

Here are the steps I took to build: mamba install -y -c conda-forge -c bioconda -c r zlib openmp minimap2 samtools pysam biopython

git clone --recurse-submodules https://github.com/refresh-bio/kmc.git 

cd kmc 

make -j32

sudo apt-get install -y libbz2-dev liblzma-dev libcurl4-openssl-dev zlib1g-dev

git clone https://github.com/samtools/htslib.git 

cd ./htslib 

autoreconf -i 

git submodule update --init --recursive 

./configure 

make 

sudo make install

git clone --recursive https://github.com/kensung-lab/hypo-assembler/ 

cd ./hypo-assembler 

./build_all.sh # -> ERROR

[joshua-casey]

Hi,

The make step that produces the error should have some error message that shows at which step it has an error. You can try piping the error to a file i.e.

./build_all.sh 2>&1 > build.log

And see in build.log if there are any error message produced, or send the file here for me to check.

Thank you.

[biogrammatics]

Different from OP, but attaching my build.log file.

build_all.sh fails to build any of the tools, seems to choke on dealing with ./suk

build.log

[biogrammatics]

I can get run_all.sh to work up until line 158 and then get the error:

./run_all.sh: line 158: ./suk: is a directory

presumably because build_all.sh should have used to ./suk directory to create executable ./suk

[petitlunette]

I have attempted to build the repo but have been met with other errors mentioned above, and am currently facing this error:

make[2]: [CMakeFiles/hypo.dir/build.make:104: CMakeFiles/hypo.dir/src/Hypo.cpp.o] Error 1 make[1]: [CMakeFiles/Makefile2:561: CMakeFiles/hypo.dir/all] Error 2 make: *** [Makefile:156: all] Error 2

Here are the steps I took to build: mamba install -y -c conda-forge -c bioconda -c r zlib openmp minimap2 samtools pysam biopython

I experienced the same error during building. I built the overlap, scaffold and suk individually according to the build_all.sh, and the polisher module would not build correctly. I got the same error: make[2]: [CMakeFiles/hypo.dir/build.make:104: CMakeFiles/hypo.dir/src/Hypo.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... make[1]: [CMakeFiles/Makefile2:561: CMakeFiles/hypo.dir/all] Error 2 make: [Makefile:156: all] Error 2

To fix, I edited the Monitor.hpp files and CMakeList.txt in the polisher folder: CMakeLists.txt Monitor.hpp

cd polisher
cd external/install/htslib
autoreconf --install
autoreconf
./configure --prefix=$(pwd) --disable-bz2 --disable-lzma
make -j 10
make install
cd ../../..
mkdir -p build
cd build
#edit monitor.hpp and cmakelists.txt
cmake -DCMAKE_BUILD_TYPE=Release ..
make -j 10

Hope this helps :)