I have also tried to compile on CentOS 7 the newest version of Augustus 3.2.2. However, now I'm getting a segmentation fault when trying to run PPX. Please help. Here is what I did for compilation.
Code: Select all
#compile filterBam, adding BAMTOOLS variable with path to bamtools
[augustus-3.2.2]$ make -C auxprogs/filterBam/src/ BAMTOOLS=/home/ngs/.linuxbrew/opt/bamtools/include/bamtools LIBZIP=true
make: Entering directory `/home/ngs/augustus-3.2.2/auxprogs/filterBam/src'
g++ -std=c++0x -c filterBam.cc -o filterBam.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -c functions/MatePairs.cc -o MatePairs.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -c functions/getReferenceName.cc -o getReferenceName.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -c functions/initOptions.cc -o initOptions.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -c functions/SingleAlignment.cc -o SingleAlignment.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -c functions/printElapsedTime.cc -o printElapsedTime.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz
filterBam compiled with BAMTOOLS=/home/ngs/.linuxbrew/opt/bamtools/include/bamtools
cp filterBam ../../../bin/filterBam
make: Leaving directory `/home/ngs/augustus-3.2.2/auxprogs/filterBam/src'
#compile rest of augustus with include path to bamtools
[augustus-3.2.2]$ make INCLUDES=/home/ngs/.linuxbrew/opt/bamtools/include/bamtools LIBZIP=true
mkdir -p bin
cd src && make
make[1]: Entering directory `/home/ngs/augustus-3.2.2/src'
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o genbank.o genbank.cc -I../include
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
from ../include/genbank.hh:26,
from genbank.cc:15:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
from ../include/genbank.hh:26,
from genbank.cc:15:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
from ../include/genbank.hh:26,
from genbank.cc:15:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o properties.o properties.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o pp_profile.o pp_profile.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o pp_hitseq.o pp_hitseq.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o pp_scoring.o pp_scoring.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o statemodel.o statemodel.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o namgene.o namgene.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o types.o types.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o gene.o gene.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o evaluation.o evaluation.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o motif.o motif.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o geneticcode.o geneticcode.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o hints.o hints.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o extrinsicinfo.o extrinsicinfo.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o projectio.o projectio.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o intronmodel.o intronmodel.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o exonmodel.o exonmodel.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o igenicmodel.o igenicmodel.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o utrmodel.o utrmodel.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o merkmal.o merkmal.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o vitmatrix.o vitmatrix.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o lldouble.o lldouble.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o mea.o mea.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o graph.o graph.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o meaPath.o meaPath.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o exoncand.o exoncand.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o randseqaccess.o randseqaccess.cc -I../include
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
from ../include/genbank.hh:26,
from randseqaccess.cc:16:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
from ../include/genbank.hh:26,
from randseqaccess.cc:16:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
from ../include/genbank.hh:26,
from randseqaccess.cc:16:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o fasta.o fasta.cc -I../include
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
from ../include/fasta.hh:18,
from fasta.cc:14:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
from ../include/fasta.hh:18,
from fasta.cc:14:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
from ../include/fasta.hh:18,
from fasta.cc:14:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o ncmodel.o ncmodel.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o commontrain.o commontrain.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o igenictrain.o igenictrain.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o introntrain.o introntrain.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o exontrain.o exontrain.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o utrtrain.o utrtrain.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o dummy.o dummy.cc -I../include
g++ -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o dummy.o -I../include -lboost_iostreams
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
from ../include/genbank.hh:26,
from augustus.cc:16:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
from ../include/genbank.hh:26,
from augustus.cc:16:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
from ../include/genbank.hh:26,
from augustus.cc:16:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
cp augustus ../bin/
g++ -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o -I../include -lboost_iostreams
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
from ../include/genbank.hh:26,
from etraining.cc:15:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
from ../include/genbank.hh:26,
from etraining.cc:15:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
from ../include/genbank.hh:26,
from etraining.cc:15:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
cp etraining ../bin/
g++ -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o prepareAlign pp_prepare_align.cc
cp prepareAlign ../bin/
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include
g++ -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -lboost_iostreams
cp fastBlockSearch ../bin/
echo "-Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -DZIPINPUT" > cxxflags
make[1]: Leaving directory `/home/ngs/augustus-3.2.2/src'
cd auxprogs && make
make[1]: Entering directory `/home/ngs/augustus-3.2.2/auxprogs'
cd bam2hints; make;
make[2]: Entering directory `/home/ngs/augustus-3.2.2/auxprogs/bam2hints'
g++ -Wall -O2 -c bam2hints.cc -o bam2hints.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools
g++ -Wall -O2 -o bam2hints bam2hints.o -lbamtools -lz
cp bam2hints ../../bin
make[2]: Leaving directory `/home/ngs/augustus-3.2.2/auxprogs/bam2hints'
cd compileSpliceCands; make;
make[2]: Entering directory `/home/ngs/augustus-3.2.2/auxprogs/compileSpliceCands'
gcc -Wall -pedantic -ansi -c compileSpliceCands.c
cc -c -o list.o list.c
gcc -o compileSpliceCands compileSpliceCands.o list.o;
make[2]: Leaving directory `/home/ngs/augustus-3.2.2/auxprogs/compileSpliceCands'
cd filterBam; make;
make[2]: Entering directory `/home/ngs/augustus-3.2.2/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory `/home/ngs/augustus-3.2.2/auxprogs/filterBam/src'
g++ -std=c++0x -c filterBam.cc -o filterBam.o /home/ngs/.linuxbrew/opt/bamtools/include/bamtools
filterBam.cc:14:31: fatal error: api/BamReader.h: No such file or directory
compilation terminated.
make[3]: *** [filterBam.o] Error 1
make[3]: Leaving directory `/home/ngs/augustus-3.2.2/auxprogs/filterBam/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/ngs/augustus-3.2.2/auxprogs/filterBam'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/ngs/augustus-3.2.2/auxprogs'
make: *** [all] Error 2
#got error on bam2hints, move into folder and recompile and then it works?
[ngs@localhost augustus-3.2.2]$ cd auxprogs/bam2hints
[ngs@localhost bam2hints]$ make INCLUDES=/home/ngs/.linuxbrew/opt/bamtools/include/bamtools LIBZIP=true
make: `bam2hints' is up to date.
[ngs@localhost bam2hints]$ make clean
rm -f bam2hints.o bam2hints ../../bin/bam2hints
[ngs@localhost bam2hints]$ make INCLUDES=/home/ngs/.linuxbrew/opt/bamtools/include/bamtools LIBZIP=true
g++ -Wall -O2 -c bam2hints.cc -o bam2hints.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools
g++ -Wall -O2 -o bam2hints bam2hints.o -lbamtools -lz
cp bam2hints ../../bin