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  • RyNkA
    Member
    • Jul 2013
    • 20

    #1

    Problem with trinity and jellyfish

    Code:
    Using gnu compiler for Inchworm and Chrysalis
    cd Inchworm && (test -e configure || autoreconf) \
                    && ./configure --prefix=`pwd`  && make install
    checking for a BSD-compatible install... /usr/bin/install -c
    checking whether build environment is sane... yes
    checking for gawk... gawk
    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
    make[1]: Entering directory `/home/rynka/trinity/Inchworm'
    Making install in src
    make[2]: Entering directory `/home/rynka/trinity/Inchworm/src'
    make[3]: Entering directory `/home/rynka/trinity/Inchworm/src'
    test -z "/home/rynka/trinity/Inchworm/bin" || mkdir -p -- "/home/rynka/trinity/Inchworm/bin"
      /usr/bin/install -c 'inchworm' '/home/rynka/trinity/Inchworm/bin/inchworm'
      /usr/bin/install -c 'cigar_tweaker' '/home/rynka/trinity/Inchworm/bin/cigar_tweaker'
      /usr/bin/install -c 'pull_reads_with_kmers' '/home/rynka/trinity/Inchworm/bin/pull_reads_with_kmers'
      /usr/bin/install -c 'FastaToDeBruijn' '/home/rynka/trinity/Inchworm/bin/FastaToDeBruijn'
      /usr/bin/install -c 'fastaToKmerCoverageStats' '/home/rynka/trinity/Inchworm/bin/fastaToKmerCoverageStats'
    make[3]: Nothing to be done for `install-data-am'.
    make[3]: Leaving directory `/home/rynka/trinity/Inchworm/src'
    make[2]: Leaving directory `/home/rynka/trinity/Inchworm/src'
    make[2]: Entering directory `/home/rynka/trinity/Inchworm'
    make[3]: Entering directory `/home/rynka/trinity/Inchworm'
    make[3]: Nothing to be done for `install-exec-am'.
    make[3]: Nothing to be done for `install-data-am'.
    make[3]: Leaving directory `/home/rynka/trinity/Inchworm'
    make[2]: Leaving directory `/home/rynka/trinity/Inchworm'
    make[1]: Leaving directory `/home/rynka/trinity/Inchworm'
    cd Chrysalis && make UNSUPPORTED=yes 
    make[1]: Entering directory `/home/rynka/trinity/Chrysalis'
    make[1]: Nothing to be done for `all'.
    make[1]: Leaving directory `/home/rynka/trinity/Chrysalis'
    cd trinity-plugins/rsem && make 
    make[1]: Entering directory `/home/rynka/trinity/trinity-plugins/rsem-1.2.3'
    g++ -Wall -O2 -c -I. parseIt.cpp
    In file included from sam/bam.h:52:0,
                     from SamParser.h:11,
                     from parseIt.cpp:26:
    sam/bgzf.h:29:18: fatal error: zlib.h: No such file or directory
    compilation terminated.
    make[1]: *** [parseIt.o] Error 1
    make[1]: Leaving directory `/home/rynka/trinity/trinity-plugins/rsem-1.2.3'
    make: *** [all] Error 2
    Hi, I got a problem running a sample, i got a error situation, i did some searching on the web and found out that i have to install libncurses5-dev,but even after i install that i still got the problem, any suggestion ?
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    Here is the important error.

    Code:
    sam/bgzf.h:29:18: fatal error: zlib.h: No such file or directory
    You need to install "zlib" library.

    Comment

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