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  • HELP! CASAVA_v1.7.0 Install error:pthread library not found

    Hi everyone,

    I've been trying to install CASAVA 1.7 and run into following errors when configuration.

    $../CASAVA_v1.7.0/src/configure

    cmake version "cmake version 2.8.0" is already installed at /usr/local/bio-soft/CASAVA_v1.7.0-build/bootstrap/bin/cmake
    nothing to be done
    Using installed /usr/local/bio-soft/CASAVA_v1.7.0-build/bootstrap/bin/cmake
    -- The C compiler identification is GNU
    -- The CXX compiler identification is GNU
    -- Check for working C compiler: /usr/bin/gcc
    -- Check for working C compiler: /usr/bin/gcc -- works
    -- Detecting C compiler ABI info
    -- Detecting C compiler ABI info - done
    -- Check for working CXX compiler: /usr/bin/c++
    -- Check for working CXX compiler: /usr/bin/c++ -- works
    -- Detecting CXX compiler ABI info
    -- Detecting CXX compiler ABI info - done
    -- install prefix: /usr/local
    -- install exec prefix: .
    -- install bin dir: ./bin
    -- install lib dir: ./lib/CASAVA-1.7.0
    -- install libexec dir: ./libexec/CASAVA-1.7.0
    -- install include dir: include/CASAVA-1.7.0
    -- install data dir: share/CASAVA-1.7.0
    -- install doc dir: doc/CASAVA-1.7.0
    -- install man dir: man
    -- Verifying target directories access
    -- Creating external tools in subdirectory opt
    -- Could NOT find Boost
    -- Boost 1.41.0 not found. Boost will be built from the distribution...
    Decompressing /usr/local/bio-soft/CASAVA_v1.7.0/src/../redist/boost_1_41_0.tar.gz
    Building Boost.Jam with toolset gcc... tools/jam/src/bin.linuxx86_64/bjam
    Unicode/ICU support for Boost.Regex?... not found.
    Backing up existing Boost.Build configuration in project-config.jam.1
    Generating Boost.Build configuration in project-config.jam...

    Bootstrapping is done. To build, run:

    ./bjam

    To adjust configuration, edit 'project-config.jam'.
    Further information:

    - Command line help:
    ./bjam --help

    - Getting started guide:


    - Boost.Build documentation:


    warning: Building Boost.Regex with the optional Unicode/ICU support disabled.
    note: Please refer to the Boost.Regex documentation for more information
    note: this is a strictly optional feature.
    ...patience...
    ...patience...
    ...found 16182 targets...
    boost-1_41_0 installed successfully
    -- Successfuly built boost 1.41.0 from the distribution package...
    -- Installing Post-Run Command Framework
    -- Check if the system is big endian
    -- Searching 16 bit integer
    -- Looking for sys/types.h
    -- Looking for sys/types.h - found
    -- Looking for stdint.h
    -- Looking for stdint.h - found
    -- Looking for stddef.h
    -- Looking for stddef.h - found
    -- Check size of unsigned short
    -- Check size of unsigned short - done
    -- Using unsigned short
    -- Check if the system is big endian - little endian
    -- Looking for floorf
    -- Looking for floorf - found
    -- Looking for round
    -- Looking for round - found
    -- Looking for roundf
    -- Looking for roundf - found
    -- Looking for powf
    -- Looking for powf - found
    -- Looking for erf
    -- Looking for erf - found
    -- Looking for erf
    -- Looking for erf - found
    -- Looking for erfc
    -- Looking for erfc - found
    -- Looking for erfc
    -- Looking for erfc - found
    -- Found ZLIB header: /usr/include/zlib.h
    -- Found ZLIB library: /usr/lib/libz.so
    -- gzip compression supported
    -- Found BZIP2 header: /usr/include/bzlib.h
    -- Found BZIP2 library: /usr/lib/libbz2.so
    -- bzip2 compression supported
    -- pthread headers: /usr/include
    -- pthread library: PTHREAD_LIBRARY-NOTFOUND
    CMake Error at cmake/macros.cmake:87 (message):
    pthread library is required to build the CASAVA
    Call Stack (most recent call first):
    cmake/cxxConfigure.cmake:84 (casava_find_boost)
    c++/CMakeLists.txt:30 (include)


    -- Configuring incomplete, errors occurred!
    Couldn't configure the project:

    /usr/local/bio-soft/CASAVA_v1.7.0-build/bootstrap/bin/cmake -H"/usr/local/bio-soft/CASAVA_v1.7.0/src" -B"/usr/local/bio-soft/CASAVA_v1.7.0-build" -G"Unix Makefiles" -DCASAVA_PREFIX:PATH= -DCASAVA_EXEC_PREFIX:PATH= -DCMAKE_INSTALL_PREFIX:PATH= -DCASAVA_BINDIR:PATH= -DCASAVA_LIBDIR:PATH= -DCASAVA_LIBEXECDIR:PATH= -DCASAVA_INCLUDEDIR:PATH= -DCASAVA_DATADIR:PATH= -DCASAVA_DOCDIR:PATH= -DCASAVA_MANDIR:PATH= -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo

    Moving CMakeCache.txt to CMakeCache.txt.removed

  • #2
    Not directly answering your question but is there a specific reason that you are trying to install pipeline v.1.7? Pipeline v.1.8 is out.

    Comment


    • #3
      Originally posted by GenoMax View Post
      Not directly answering your question but is there a specific reason that you are trying to install pipeline v.1.7? Pipeline v.1.8 is out.
      I have installed V1.8 , but some related scripts prefer v.1.7. Thank you for your replies.

      Regards,

      Comment


      • #4
        Originally posted by GenoMax View Post
        Not directly answering your question but is there a specific reason that you are trying to install pipeline v.1.7? Pipeline v.1.8 is out.
        The CASAVA 1.7 output is Illumina 1.3+ FASTQ format, Our script only support that format. However, CASAVA 1.8 gives out Sanger FASTQ files. I want to know if the CASAVA 1.8 FASTQ format supported by SOAP denovo and BWA directly?

        Comment


        • #5
          Hi Soofree -

          I'm having the same issue - any resolution?

          Dweeb

          Comment


          • #6
            --static

            I ran into the same problem when I used --static while running configure. Removed --static and now it is past that step.

            Comment


            • #7
              Lots of information but the critical lines here are

              -- pthread library: PTHREAD_LIBRARY-NOTFOUND
              CMake Error at cmake/macros.cmake:87 (message):
              pthread library is required to build the CASAVA

              You need the pthread library.

              Comment


              • #8
                Ho yeah, I am back with solutions:

                In linux, try following two lines in termnal:

                sudo ln -s /usr/lib/x86_64_linux_gun/lib2.so /usr/lib
                sudo ln -s /usr/lib/x86_64_linux_gun/libpth* /usr/lib

                Comment


                • #9
                  The two link commands worked for me. Just make sure you don't copy and paste as they both say 'gun' instead of 'gnu'

                  Comment

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