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Fatal Error in Augustus installation on Mac #9

@mtajhuss

Description

@mtajhuss

I have installed bamtools followed by the Augustus. But having the issue in of bam2hint and api/bamreader not found. I tried to follow the instruction other suggested having similar problem e.g. 1 and 2.

I edited the bam2hint make file with the correct bamtools pathway. and also checked the bamreader file which is available under the bamtools pathway i.e "bamtools/src/api/BamReader.h"

auxprogs/bam2hints/Makefile

BAMTOOLS=Documents/packages/bamtools

INCLUDES = $(BAMTOOLS)/include/bamtools

But still the following error arises.

make CC=gcc-9 CXX=g++-9 BAMTOOLS_CC=clang BAMTOOLS_CXX=clang++ BAMTOOLS=Documents/packages/bamtools mkdir -p bin cd src && /Applications/Xcode.app/Contents/Developer/usr/bin/make CC=gcc-9 CXX=g++-9 echo "-Wall -Wno-sign-compare -ansi -pedantic -O3 " > cflags cd auxprogs && /Applications/Xcode.app/Contents/Developer/usr/bin/make CC=clang CXX=clang++ BAMTOOLS=Documents/packages/bamtools cd bam2hints; make CXX=clang++ CC=clang BAMTOOLS=Documents/packages/bamtools; clang++ -Wall -O0 -g -ggdb -c bam2hints.cc -o bam2hints.o -IDocuments/packages/bamtools/include/bamtools bam2hints.cc:16:10: fatal error: 'api/BamReader.h' file not found #include <api/BamReader.h> ^~~~~~~~~~~~~~~~~ 1 error generated. make[2]: *** [bam2hints.o] Error 1 make[1]: *** [all] Error 2 make: *** [all] Error 2

how to fix this issue?

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