search

BenLangmead / bowtie2

A fast and sensitive gapped read aligner
GNU General Public License v3.0
683 stars 159 forks source link

LIBNCBI_NGS-NOFOUND #482

Open mdsimguy opened 4 months ago

mdsimguy commented 4 months ago

make bowtie2-build-s USE_SAIS_OPENMP=1 [ 18%] Built target libsais_project [ 36%] Built target ncbi_vdb_project [ 59%] Built target ngs_project [ 59%] Building CXX object CMakeFiles/bowtie2-build-s.dir/bt2_build.cpp.o [ 63%] Building CXX object CMakeFiles/bowtie2-build-s.dir/diff_sample.cpp.o [ 63%] Building CXX object CMakeFiles/bowtie2-build-s.dir/bowtie_build_main.cpp.o [ 68%] Building CXX object CMakeFiles/bowtie2-build-s.dir/ccnt_lut.cpp.o [ 68%] Building CXX object CMakeFiles/bowtie2-build-s.dir/ref_read.cpp.o [ 72%] Building CXX object CMakeFiles/bowtie2-build-s.dir/alphabet.cpp.o [ 72%] Building CXX object CMakeFiles/bowtie2-build-s.dir/shmem.cpp.o [ 77%] Building CXX object CMakeFiles/bowtie2-build-s.dir/edit.cpp.o [ 81%] Building CXX object CMakeFiles/bowtie2-build-s.dir/bt2_idx.cpp.o [ 81%] Building CXX object CMakeFiles/bowtie2-build-s.dir/bt2_io.cpp.o [ 86%] Building CXX object CMakeFiles/bowtie2-build-s.dir/bt2_locks.cpp.o [ 86%] Building CXX object CMakeFiles/bowtie2-build-s.dir/bt2_util.cpp.o [ 90%] Building CXX object CMakeFiles/bowtie2-build-s.dir/reference.cpp.o [ 90%] Building CXX object CMakeFiles/bowtie2-build-s.dir/ds.cpp.o [ 95%] Building CXX object CMakeFiles/bowtie2-build-s.dir/multikey_qsort.cpp.o [ 95%] Building CXX object CMakeFiles/bowtie2-build-s.dir/limit.cpp.o [100%] Building CXX object CMakeFiles/bowtie2-build-s.dir/random_source.cpp.o make[3]: No rule to make target 'LIBNCBI_NGS-NOTFOUND', needed by 'bowtie2-build-s'. Stop. make[2]: [CMakeFiles/Makefile2:991: CMakeFiles/bowtie2-build-s.dir/all] Error 2 make[1]: [CMakeFiles/Makefile2:998: CMakeFiles/bowtie2-build-s.dir/rule] Error 2 make: [Makefile:608: bowtie2-build-s] Error 2

ch4rr0 commented 4 months ago

Hello,

It seems like you are trying to build bowtie2-build-s with libsais support using the CMake build system. If that is the case then you will need to issue the following command in order to do so. cmake . -DUSE_SAIS=1 && make bowtie2-build-s

If on the other hand you are trying to build with the standard Makefile then use: make libsais USE_SAIS_OPENMP=1 && make bowtie2-build-s USE_SAIS_OPENMP=1

I am not sure why the CMake build file is complaining out libngs unless you trying to link to this library also.

Please let me know your use-case. I will be happy to help resolve any issues.