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  • Trinity installation error on Mac OSX Marvericks

    I would like to install trinity on my iMac witn Mac OSX 10.9.2 (Mavericks).
    After untaring trinity (trinityrnaseq_r20131110), $ make command gives an error.
    below is in the terminal window:
    Using gnu compiler for Inchworm and Chrysalis
    cd Inchworm && (test -e configure || autoreconf) \
    && ./configure --prefix=`pwd` && /Applications/Xcode.app/Contents/Developer/usr/bin/make install
    checking for a BSD-compatible install... /usr/bin/install -c
    checking whether build environment is sane... yes
    checking for gawk... no
    checking for mawk... no
    checking for nawk... no
    checking for awk... awk
    checking whether make sets $(MAKE)... yes
    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 for style of include used by make... GNU
    checking dependency style of g++... gcc3
    checking for library containing cos... none required
    configure: creating ./config.status
    config.status: creating Makefile
    config.status: creating src/Makefile
    config.status: creating config.h
    config.status: config.h is unchanged
    config.status: executing depfiles commands
    Making install in src
    if g++ -DHAVE_CONFIG_H -I. -I. -I.. -pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated -m64 -g -O2 -MT Fasta_entry.o -MD -MP -MF ".deps/Fasta_entry.Tpo" -c -o Fasta_entry.o Fasta_entry.cpp; \
    then mv -f ".deps/Fasta_entry.Tpo" ".deps/Fasta_entry.Po"; else rm -f ".deps/Fasta_entry.Tpo"; exit 1; fi
    clang: warning: argument unused during compilation: '-fopenmp'
    if g++ -DHAVE_CONFIG_H -I. -I. -I.. -pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated -m64 -g -O2 -MT IRKE_run.o -MD -MP -MF ".deps/IRKE_run.Tpo" -c -o IRKE_run.o IRKE_run.cpp; \
    then mv -f ".deps/IRKE_run.Tpo" ".deps/IRKE_run.Po"; else rm -f ".deps/IRKE_run.Tpo"; exit 1; fi
    clang: warning: argument unused during compilation: '-fopenmp'
    IRKE_run.cpp:9:10: fatal error: 'omp.h' file not found
    #include <omp.h>
    ^
    1 error generated.
    make[2]: *** [IRKE_run.o] Error 1
    make[1]: *** [install-recursive] Error 1
    make: *** [inchworm_target] Error 2


    Does anyone know how to properly install trinity on Mavericks?
    I have bowtie1 and bowtie2 installed on the iMac.
    Thanks for your help in advance.

    Agrias

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