Augustus installation error on MacOS

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Tajammul Hussain
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Joined: Wed Apr 22, 2020 5:01 pm

Augustus installation error on MacOS

Post by Tajammul Hussain » Mon Apr 27, 2020 7:53 pm

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. [https://www.biostars.org/p/189048/][/1] and [https://iamphioxus.org/tag/bamtools/][/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"

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auxprogs/bam2hints/Makefile

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BAMTOOLS=Documents/packages/bamtools

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INCLUDES = $(BAMTOOLS)/include/bamtools
But still the following error arises.

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make CC=gcc-9 CXX=g++-9 BAMTOOLS_CC=clang BAMTOOLS_CXX=clang++ BAMTOOLS=Documents/packages/bamtools

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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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