Unable to configure due to bamtools dependency

[michaelbarton]

I am currently getting this error:

configure: error: The bamtools library must be installed (http://github.com/pezmaster31/bamtools). You can specify its path with the --with-bamtools=PATH option

I have tried running this command both of these two ways:

CXXFLAGS="-I/usr/include/bamtools" ./configure

Or

./configure --with-bamtools=/usr/include/bamtools/

The contents of /usr/include/bamtools/ is:

drwxr-xr-x  3 root root 4096 Nov 18 00:28 api
drwxr-xr-x  2 root root 4096 Nov 18 00:28 shared
-rw-r--r--  1 root root  852 Aug  7 21:01 bamtools_version.h

The contents of /usr/include/bamtools/api is:

drwxr-xr-x 2 root root  4096 Nov 18 00:28 algorithms
-rw-r--r-- 1 root root 23779 Aug  7 21:01 BamAlignment.h
-rw-r--r-- 1 root root 15082 Aug  7 21:01 BamAux.h
-rw-r--r-- 1 root root   847 Jul  5  2016 BamAlgorithms.h
-rw-r--r-- 1 root root  9682 Jul  5  2016 BamConstants.h
-rw-r--r-- 1 root root  2885 Jul  5  2016 BamIndex.h
-rw-r--r-- 1 root root  4676 Jul  5  2016 BamMultiReader.h
-rw-r--r-- 1 root root  4285 Jul  5  2016 BamReader.h
-rw-r--r-- 1 root root  2208 Jul  5  2016 BamWriter.h
-rw-r--r-- 1 root root  3022 Jul  5  2016 IBamIODevice.h
-rw-r--r-- 1 root root  3725 Jul  5  2016 SamConstants.h
-rw-r--r-- 1 root root  2959 Jul  5  2016 SamHeader.h
-rw-r--r-- 1 root root  2389 Jul  5  2016 SamProgram.h
-rw-r--r-- 1 root root  3127 Jul  5  2016 SamProgramChain.h
-rw-r--r-- 1 root root  3449 Jul  5  2016 SamReadGroup.h
-rw-r--r-- 1 root root  3281 Jul  5  2016 SamReadGroupDictionary.h
-rw-r--r-- 1 root root  2567 Jul  5  2016 SamSequence.h
-rw-r--r-- 1 root root  3248 Jul  5  2016 SamSequenceDictionary.h
-rw-r--r-- 1 root root   757 Jul  5  2016 api_global.h

Any assistance you can provide is appreciated.

[mpre]

Hi Michael,
this seems to happen in sga too (e.g., this issue ).
Anyway, usually ./configure --with-bamtools=/usr works for me. Can you try it?

[michaelbarton]

Thanks for following up Marco. That fixed it. I appreciate your help with this.

I now however get the error:

g++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Thirdparty -fopenmp  -I/usr/include -I/usr/include/bamtools -Wall -Wextra  -Wno-unknown-pragmas -O3 -MT libutil_a-ClusterReader.o -MD -MP -MF .deps/libutil_a-ClusterReader.Tpo -c -o libutil_a-ClusterReader.o `test -f 'ClusterReader.cpp' || echo './'`ClusterReader.cpp
ClusterReader.cpp: In member function 'bool ClusterReader::readCluster(ClusterRecord&)':
ClusterReader.cpp:70:41: error: cannot convert 'std::basic_istream<char>' to 'bool' in initialization
     bool good = getline(*m_pReader, line);
                                         ^
make[2]: *** [libutil_a-ClusterReader.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
Makefile:718: recipe for target 'libutil_a-ClusterReader.o' failed
make[2]: Leaving directory '/tmp/fsga/Util'
Makefile:359: recipe for target 'all-recursive' failed
make[1]: Leaving directory '/tmp/fsga'
Makefile:300: recipe for target 'all' failed
The command '/bin/sh -c fsga.sh' returned a non-zero code: 2

[michaelbarton]

I'm building a docker file here, if that is useful:
https://github.com/bioboxes/fast-sga/tree/feature/add-fsg-version

[mpre]

Thank you for reporting this Michael.
I tried to compile fsg on ubuntu 17.10 and I get the same error when using g++ versions 6 and 7. Indeed, by the c++11 standard the conversion from std::basic_ios to bool should be explicit (see this link for more ).
I can compile the tool if I set g++-5 as default (sudo update-alternatives --config g++ on ubuntu, I'm not sure if other Linux distributions provide the same tool). As a quick (and "dirty") workaround you could use that version of g++ to get fsg compiling.

Note that the error you get is in the sga codebase (the code we wrote is in src/FSG) so we should probably update the version we are distributing. Unfortunately, the developers of that tool chose to follow the g++-98 standard (see this commit) but we can't do the same since I'm pretty sure we use lambdas somewhere in src/FSG. Therefore, integrating the last commits of sga in fsg could require some time.

[michaelbarton]

This was what was exactly needed to resolve this. Thank you for you help.