MIssing ncbi/NGS.hpp

[mykmilligan]

Hello, I get an error when making ngs-tools: fatal error: ngs/ncbi/NGS.hpp: No such file or directory

Here is my make output. Where can I find NGS.hpp?

make
cd /root/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj; cmake -DCMAKE_ARCHIVE_OUTPUT_DIRECTORY=/root/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/ilib -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/root/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/lib -DCMAKE_RUNTIME_OUTPUT_DIRECTORY=/root/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/bin -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/work/apps/ngstools/3.1.1/bin/.. -DCMAKE_C_COMPILER=/work/apps/gcc/9.4.0/bin/gcc -DCMAKE_CXX_COMPILER=/work/apps/gcc/9.4.0/bin/g++ -DVDB_INCDIR=/work/apps/ncbi/ncbi-vdb/include -DVDB_LIBDIR=/work/apps/ncbi/ncbi-vdb/lib64 -DVDB_ILIBDIR= -DSRATOOLS_SRCDIR= -DSRATOOLS_BINDIR= -DVERSION=3.1.1 -DMAJVERS=3 -DPLATFORM=x86_64 -DOUTDIR=/root/ncbi-outdir/ngs-tools/.. /share/apps/src/ncbi/ngs-tools
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.

Update the VERSION argument value or use a ... suffix to tell
CMake that the project does not need compatibility with older versions.

CMAKE_VERSION=3.27.4
CMAKE_CXX_STANDARD=11
CMake Warning at build/env.cmake:180 (message):
Failed to locate 'ant' executable in PATH or ANT_HOME. Please specify path
to 'ant' via ANT_EXECUTABLE
Call Stack (most recent call first):
CMakeLists.txt:31 (include)

CMake Warning at build/env.cmake:213 (message):
NGS includes are not found in /ngs/ngs-sdk.
Call Stack (most recent call first):
CMakeLists.txt:31 (include)

-- Found NCBI-VDB includes in /work/apps/ncbi/ncbi-vdb/include. Looking for NCBI-VDB libraries...
-- Configuring done (0.1s)
-- Generating done (0.3s)
-- Build files have been written to: /root/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj
make -C /root/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/ --no-print-directory
[ 1%] Building C object libs/tk-version/src/CMakeFiles/tk-version.dir/toolkit.vers.c.o
[ 2%] Linking C static library /root/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/ilib/libtk-version.a
[ 2%] Built target tk-version
[ 4%] Building CXX object tools/dump_ref_fasta/CMakeFiles/dump-ref-fasta.dir/DumpReferenceFASTA.cpp.o
/share/apps/src/ncbi/ngs-tools/tools/dump_ref_fasta/DumpReferenceFASTA.cpp:27:10: fatal error: ngs/ncbi/NGS.hpp: No such file or directory
27 | #include <ngs/ncbi/NGS.hpp>
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [tools/dump_ref_fasta/CMakeFiles/dump-ref-fasta.dir/DumpReferenceFASTA.cpp.o] Error 1
make[2]: *** [tools/dump_ref_fasta/CMakeFiles/dump-ref-fasta.dir/all] Error 2
make[1]: *** [all] Error 2
make: *** [cmake] Error 2

[klymenko]

Update ncbi-vdb, sra-tools and and ngs-tools.
It is recommended to have them in the same directory, next to each other.
For each of those repositories, run:
../configure && make

[mykmilligan]

Thanks for your help. Putting all the tools in one directory solved the error.