No BAM tools support, even when specifying directories

[charcuterie]

./configure --with-bam_tools_headers="/storage/Software/bamtools/20140828/include/" --with-bam_tools_library="/storage/Software/bamtools/20140828/lib/"

Attempted to configure as above. I end up without BAM support after receiving the following warning:

configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library

Full output:

$ ./configure --with-bam_tools_headers="/storage/Software/bamtools/20140828/include/" --with-bam_tools_library="/storage/Software/bamtools/20140828/lib/"
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
provided BAMTools headers directory is /storage/Software/bamtools/20140828/include/
provided BAMTools library directory is /storage/Software/bamtools/20140828/lib/
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether we're compiling on Darwin/MacOS... no
checking for cos in -lm... yes
checking for cblas_dgemm in -lgslcblas... yes
checking for gsl_blas_dgemm in -lgsl... yes
checking for linking against gsl matrix... yes
checking for BAMTools... no
configure: WARNING: could not find BAMTools, disabling BAM support
configure: creating ./config.status
config.status: creating Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
config.status: creating src/common/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
config.status: creating src/common/Makefile
config.status: creating src/common/config.hpp
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
config.status: creating src/common/Makefile
config.status: creating src/common/config.hpp
config.status: creating src/test/regressionTests.xml
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library

[rekado]

with-bam_tools_library should point at the bam library, not just the directory. Works for me in the package I made for GNU Guix.

[lcscs12345]

Do this before running ./configure [options]
BAM_LIBRARIES_DIR=LD_LIBRARY_PATH
export LD_LIBRARY_PATH="/path/to/bamtools/lib"

[fabou-uobaf]

Hello
I experience exactly the same issue. If I call
./configure --with-bam_tools_headers="${HOME}/.local/include/bamtools/" --with-bam_tools_library="${HOME}/.local/lib64/"

I get:
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
provided BAMTools headers directory is ${HOME}/.local/include/bamtools/
provided BAMTools library directory is ${HOME}/.local/lib64/
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether we're compiling on Darwin/MacOS... no
checking for cos in -lm... yes
checking for cblas_dgemm in -lgslcblas... yes
checking for gsl_blas_dgemm in -lgsl... yes
checking for linking against gsl matrix... yes
checking for BAMTools... no
configure: WARNING: could not find BAMTools, disabling BAM support
configure: creating ./config.status
config.status: creating Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
config.status: creating src/common/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
config.status: creating src/common/Makefile
config.status: creating src/common/config.hpp
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
config.status: creating src/common/Makefile
config.status: creating src/common/config.hpp
config.status: creating src/test/regressionTests.xml
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library

bamtools 2.5.1 is installed and the content of the lib and include directories are:
tree ${HOME}/.local/include/bamtools/
${HOME}/.local/include/bamtools/
├── api
│   ├── algorithms
│   │   └── Sort.h
│   ├── api_global.h
│   ├── BamAlgorithms.h
│   ├── BamAlignment.h
│   ├── BamAux.h
│   ├── BamConstants.h
│   ├── BamIndex.h
│   ├── BamMultiReader.h
│   ├── BamReader.h
│   ├── BamWriter.h
│   ├── IBamIODevice.h
│   ├── SamConstants.h
│   ├── SamHeader.h
│   ├── SamProgramChain.h
│   ├── SamProgram.h
│   ├── SamReadGroupDictionary.h
│   ├── SamReadGroup.h
│   ├── SamSequenceDictionary.h
│   └── SamSequence.h
└── shared
└── bamtools_global.h

tree ${HOME}/.local/lib64/
${HOME}/.local/lib64/
├── libbamtools.a
└── pkgconfig
└── bamtools-1.pc

I tried the the hints above, but nothing worked. Any help highly appreciated. Thanks in advance.

[zhengzhanye]

Hello
I experience exactly the same issue. If I call
./configure --with-bam_tools_headers="${HOME}/.local/include/bamtools/" --with-bam_tools_library="${HOME}/.local/lib64/"

I get:
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
provided BAMTools headers directory is ${HOME}/.local/include/bamtools/
provided BAMTools library directory is ${HOME}/.local/lib64/
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether we're compiling on Darwin/MacOS... no
checking for cos in -lm... yes
checking for cblas_dgemm in -lgslcblas... yes
checking for gsl_blas_dgemm in -lgsl... yes
checking for linking against gsl matrix... yes
checking for BAMTools... no
configure: WARNING: could not find BAMTools, disabling BAM support
configure: creating ./config.status
config.status: creating Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
config.status: creating src/common/Makefile
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
config.status: creating src/common/Makefile
config.status: creating src/common/config.hpp
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/test/Makefile
config.status: creating src/progs/Makefile
config.status: creating src/common/Makefile
config.status: creating src/common/config.hpp
config.status: creating src/test/regressionTests.xml
configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library

bamtools 2.5.1 is installed and the content of the lib and include directories are:
tree ${HOME}/.local/include/bamtools/
${HOME}/.local/include/bamtools/
├── api
│   ├── algorithms
│   │   └── Sort.h
│   ├── api_global.h
│   ├── BamAlgorithms.h
│   ├── BamAlignment.h
│   ├── BamAux.h
│   ├── BamConstants.h
│   ├── BamIndex.h
│   ├── BamMultiReader.h
│   ├── BamReader.h
│   ├── BamWriter.h
│   ├── IBamIODevice.h
│   ├── SamConstants.h
│   ├── SamHeader.h
│   ├── SamProgramChain.h
│   ├── SamProgram.h
│   ├── SamReadGroupDictionary.h
│   ├── SamReadGroup.h
│   ├── SamSequenceDictionary.h
│   └── SamSequence.h
└── shared
└── bamtools_global.h

tree ${HOME}/.local/lib64/
${HOME}/.local/lib64/
├── libbamtools.a
└── pkgconfig
└── bamtools-1.pc

I tried the the hints above, but nothing worked. Any help highly appreciated. Thanks in advance.

Do you have solved this problem? I meet this same problem as you,hope for a reply. Thanks!

[fabou-uobaf]

@zhanyezheng
Did not solve it. I went the detour via sam file generation.

[zhengzhanye]

@zhanyezheng
Did not solve it. I went the detour via sam file generation.

Can you tell me what method did you use ? How to finish RIP-seq call peak ? Thank you very much !

[AMChalkie]

I also have the same error with the configure script on unix.

configure: WARNING: unrecognized options: --with-bam_tools_headers, --with-bam_tools_library