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  • Problem compiling bcl2fastq-1.8.4

    Hello!

    I am trying to compile bcl2fastq on a server where I cannot be root and should be installed in a specific folder (server is under CentOS 6.5).

    I followed the manual's insctructions.

    First I downloaded the tarball:

    Code:
    wget ftp://webdata:[email protected]/Downloads/Software/bcl2fastq/bcl2fastq-1.8.4.tar.bz2
    Then created some variables:

    Code:
    export TMP=/tmp
    export SOURCE=${TMP}/bcl2fastq-1.8.4
    export BUILD=${TMP}/bcl2fastq-1.8.4-build
    export INSTALL=/software/bcl2fastq/bcl2fastq-1.8.4
    Then I extracted the files:

    Code:
    cd ${TMP}
    tar xjf /software/bcl2fastq/bcl2fastq-1.8.4.tar.bz2
    mv bcl2fastq bcl2fastq-1.8.4
    Then I ran the configuration:
    Code:
    mkdir ${BUILD}
    cd ${BUILD}
    ${SOURCE}/src/configure --prefix=${INSTALL}
    But at this step I encounter an error, at 93% of the compilation :
    Code:
    Linking CXX executable ../bin/ccmake
    /software6/apps/buildtools/20140527/bin/ld: CMakeFiles/ccmake.dir/CursesDialog/cmCursesMainForm.o: undefined reference to symbol 'keypad'
    /lib64/libtinfo.so.5: error adding symbols: DSO missing from command line
    Do you have any idea to solve the problem?

    Cheers!

  • #2
    https://www.centos.org/forums/viewtopic.php?t=6469.

    See if this works:

    Code:
    $ export LDFLAGS="$LDFLAGS -ltinfo"
    and recompile.

    Comment


    • #3
      TIP OF THE HAT to you!

      The compilation could get going.

      A new hurdle has come, with Boost.

      At the end of the compilation, I can see that Boost has been successfully installed:

      Code:
      boost-1_44_0 installed successfully
      -- Successfuly built boost 1.44.0 from the distribution package...
      But few lines down:

      Code:
      CMake Error at /tmp/bcl2fastq-1.8.4-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:1128 (message):
        Unable to find the requested Boost libraries.
      
        Boost version: 1.44.0
      
        Boost include path: /tmp/bcl2fastq-1.8.4-build/opt/bootstrap/include
      
        The following Boost libraries could not be found:
      
                boost_thread
      
        Some (but not all) of the required Boost libraries were found.  You may
        need to install these additional Boost libraries.  Alternatively, set
        BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT
        to the location of Boost.
      I found this : http://stackoverflow.com/questions/1...-finding-boost

      So I am trying to recompile using --static parameter of configure.

      Comment


      • #4
        New stop on the compilation :

        Code:
        ...
        -- All libraries will be statically linked
        -- Found ZLIB  header: /usr/include/zlib.h
        -- Found ZLIB library: /usr/lib64/libz.a
        -- gzip compression supported
        CMake Error at cmake/cxxConfigure.cmake:84 (message):
          No support for bzip2 compression
        I found other threads with the similar problem, but when installing on Ubuntu.
        I have bzip2 installed:

        Code:
        $ rpm -qa | grep bzip
        bzip2-1.0.5-7.el6_0.x86_64
        bzip2-libs-1.0.5-7.el6_0.x86_64
        bzip2-devel-1.0.5-7.el6_0.x86_64
        $ ls -lh /usr/lib64/libbz2.so 
        lrwxrwxrwx 1 root root 23 28 oct.  10:55 /usr/lib64/libbz2.so -> ../../lib64/libbz2.so.1
        How can I make the configure script to see it?
        Last edited by emixaM; 12-17-2014, 11:50 AM.

        Comment


        • #5
          Can you add /lib64 to LD_LIBRARY_PATH and try re-compiling?

          Comment


          • #6
            I did :

            Code:
            $ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/lib64"
            Then :

            Code:
            $ ${SOURCE}/src/configure --prefix=${INSTALL} --static
            But :

            Code:
            CMake Error at cmake/cxxConfigure.cmake:84 (message):
              No support for bzip2 compression
            Should I delete the building folder to re-compile? Because it went straight to the Boost compilation :

            Code:
            cmake version "cmake version 2.8.4" is already installed at /tmp/bcl2fastq-1.8.4-build/bootstrap/bin/cmake
            nothing to be done
            Using installed /tmp/bcl2fastq-1.8.4-build/bootstrap/bin/cmake

            Comment


            • #7
              Do a "make clean" and try again. I have a feeling it is not going to help.

              Probably pretty late in France so we can take this up tomorrow in case no one else comes along with a brilliant answer between now and tomorrow.

              Comment


              • #8


                I moved to Canada, and forgot to update the details!

                Currently re-compiling...

                Comment


                • #9
                  ...and it did not work.

                  Comment


                  • #10
                    Let me think some more (till later this evening). If you manage to complete the compilation in the meanwhile post an update.

                    Comment


                    • #11
                      Do you find a
                      /usr/include/bzlib.h
                      just like you find the header for the gzip compression?

                      Comment


                      • #12
                        Actually I am just at the step of the configure script. I am trying to solve the libraries links. I am sure that it is not the bzip2 library that is problematic here, but something with boost thread and GCC version. I will keep you updated.

                        Comment


                        • #13
                          What version of gcc are you using?

                          Comment


                          • #14
                            Originally posted by GenoMax View Post
                            What version of gcc are you using?
                            Good point, I had severe problems compiling with gcc 4.7.1 due to some issues in combination with boost 1.44 ..

                            Comment


                            • #15
                              I tried the oldest gcc on my system, it did not work :

                              Code:
                              C compiler on this system is: /compilers/gcc/4.6/bin/gcc 
                              C++ compiler on this system is: /compilers/gcc/4.6/bin/g++
                              And in the end :

                              Code:
                              CMake Error at cmake/cxxConfigure.cmake:84 (message):
                                No support for bzip2 compression

                              Comment

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