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This page was last updated on Sunday, 21-Dec-2014 10:17:16 CST

Installation notes for bamtools version v2.3.0

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Prerequisites

cmake
$ sudo apt-get install cmake

Installation

  1. $ cd /programinstallers/
  2. $ git clone https://github.com/pezmaster31/bamtools
  3. $ cd bamtools
  4. $ mkdir build
  5. $ cd build
  6. $ cmake ..
  7. $ make
  8. $ sudo make install
    Install the project...
    -- Install configuration: "Release"
    -- Installing: /usr/local/include/bamtools/shared/bamtools_global.h
    -- Installing: /usr/local/lib/bamtools/libbamtools.so.2.3.0
    -- Installing: /usr/local/lib/bamtools/libbamtools.so
    -- Installing: /usr/local/lib/bamtools/libbamtools.a
    -- Installing: /usr/local/include/bamtools/api/api_global.h
    -- Installing: /usr/local/include/bamtools/api/BamAlgorithms.h
    -- Installing: /usr/local/include/bamtools/api/BamAlignment.h
    -- Installing: /usr/local/include/bamtools/api/BamAux.h
    -- Installing: /usr/local/include/bamtools/api/BamConstants.h
    -- Installing: /usr/local/include/bamtools/api/BamIndex.h
    -- Installing: /usr/local/include/bamtools/api/BamMultiReader.h
    -- Installing: /usr/local/include/bamtools/api/BamReader.h
    -- Installing: /usr/local/include/bamtools/api/BamWriter.h
    -- Installing: /usr/local/include/bamtools/api/IBamIODevice.h
    -- Installing: /usr/local/include/bamtools/api/SamConstants.h
    -- Installing: /usr/local/include/bamtools/api/SamHeader.h
    -- Installing: /usr/local/include/bamtools/api/SamProgram.h
    -- Installing: /usr/local/include/bamtools/api/SamProgramChain.h
    -- Installing: /usr/local/include/bamtools/api/SamReadGroup.h
    -- Installing: /usr/local/include/bamtools/api/SamReadGroupDictionary.h
    -- Installing: /usr/local/include/bamtools/api/SamSequence.h
    -- Installing: /usr/local/include/bamtools/api/SamSequenceDictionary.h
    -- Installing: /usr/local/include/bamtools/api/algorithms/Sort.h
    -- Installing: /usr/local/bin/bamtools-2.3.0
    -- Installing: /usr/local/bin/bamtools
    -- Removed runtime path from "/usr/local/bin/bamtools-2.3.0"
  9. In the event of this error:
    $ bamtools
    bamtools: error while loading shared libraries: libbamtools.so.2.3.0: cannot open shared object file: No such file or directory
    we need to add the bamtools library path to LD_LIBRARY_PATH
    $ sudo nano /etc/profile
    ...
    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib/bamtools"
    ...
  10. Cleanup
    $ cd ../..
  11. $ rm bamtools -rf