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problems configuring installation of Bcl2fastq

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  • problems configuring installation of Bcl2fastq

    I want to install Bcl2fastq on my system running Ubuntu 14.04.2 LTS. I have admin rights.

    However the configure step always aborts with an error.

    After running configure I first ran into the typical Error messages of "No support for gzip compression" and "No support for bzip2 compression", so i followed early recommendations here and here, and copied "", "libpthread*" and "" from /usr/lib/x86_64-linux-gnu/ to /usr/lib.

    after that, running "configure" produced this new error message:
    CMake Error at cmake/cxxConfigure.cmake:95 (message):
      libxml2 was not found
    As this problem has not been discussed earlier, I tried to use the same approach by copying the libxml2-associated files to /user/lib using the following command:
    sudo cp /usr/lib/x86_64-linux-gnu/libxml2* /usr/local/lib
    As this did not help I followed the setup instruction at the end of this thread and this very helpful setup-script to ensure that all dependancies are met.

    However I still get the same error message:
    -- Could NOT find LibXml2 (missing:  LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR) 
    CMake Error at cmake/cxxConfigure.cmake:95 (message):
      libxml2 was not found
    Call Stack (most recent call first):
      c++/CMakeLists.txt:33 (include)
    -- Configuring incomplete, errors occurred!
    Couldn't configure the project:
    /tmp/bcl2fastq-build/bootstrap/bin/cmake -H"/tmp/bcl2fastq/src" -B"/tmp/bcl2fastq-build" -G"Unix Makefiles"  -DCASAVA_PREFIX:PATH=/usr/local/tools/bcl2fastq-1.8.4 -DCASAVA_EXEC_PREFIX:PATH= -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/tools/bcl2fastq-1.8.4 -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
    Any suggestions?

  • #2
    Start with

    $ sudo apt-get install libxml2 libxml2-dev
    see if that fixes the error.


    • #3
      Thanks a lot!
      I was sure I had libxml2 installed, but i seem to have been mistaken...
      Configure now completed without errors. However, now I run into the following errors during "make" at 51%
      [ 51%] Building CXX object c++/lib/io/CMakeFiles/casava_io.dir/PtreeXml.cpp.o
      /tmp/bcl2fastq/src/c++/lib/io/PtreeXml.cpp: In function ‘std::ostream& casava::io::operator<<(std::ostream&, const ptree&)’:
      /tmp/bcl2fastq/src/c++/lib/io/PtreeXml.cpp:123:123: error: no matching function for call to ‘xml_writer_make_settings(char, int)’
               boost::property_tree::write_xml(os, treeWithIndexAttributes, boost::property_tree::xml_writer_make_settings(' ', 2));
      The final error message is:
      make[2]: *** [c++/lib/io/CMakeFiles/casava_io.dir/PtreeXml.cpp.o] Error 1
      make[1]: *** [c++/lib/io/CMakeFiles/casava_io.dir/all] Error 2
      make: *** [all] Error 2
      boost is definitively installed. Do you have suggestions for this also?


      • #4
        Might be an issue with your Boost version. From a different topic, but similar error:

        I was able to install successfuly with Boost 1.55


        • #5
          I have boost version 1.54 installed, which seems to be the newest version of boost in the official Ubuntu repositories.
          So I guess that means I should download the most current version of boost directly and compile it manually?
          I'll try.


          • #6
            Illumina software is picky about version of boost libraries. A local copy here is using boost v.1.44 (which the software built itself).


            • #7
              Hi, everyone.
              while trying to figure out how to install which boost library, I simultaneously tried the alternative approach of installing via the Illumina-supplied rpm-package using the instructions here

              This now works fine, once expat-2.1.0 and xml-parser-2.41 were installed.

              So right now, I am abandoning trying to compile bcl2fastq from source and just work with the successfully installed rpm-package version.

              Thanks everyone!


              • #8
                This is for the latest bcl2fastq version 2.20.0 but it seems to be a similar error.