kensung-lab / hypo-assembler

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Make Errors #11

Open iPsychonaut opened 7 months ago

iPsychonaut commented 7 months ago

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 commented 7 months ago

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 commented 6 months ago

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 commented 6 months ago

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 commented 5 months ago

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 :)

EddieLee08 commented 3 months ago

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 :)

That really works. Thanks a lot!