This page was last updated on Sunday, 13-Nov-2016 10:10:45 CST

Installation notes for BreakDancer version 1.4.1-unstable-46-176af3e-dirty (commit 176af3e-dirty)

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Notes on earlier version 1.1

Prerequisites

• Perl modules
  • Statistics::Descriptive
  • Math::CDF
  • GD::Graph::histogram
  $ sudo cpan Statistics::Descriptive Math::CDF GD::Text::Align GD::Graph::bars GD::Graph::histogram
• Samtools development version. See samtools install notes.
  Header files are located in /usr/lib/samtools/
• Boost version 1.48 (or newer)
  Ubuntu install $ sudo apt-get install libboost-all-dev
  Fedora (I have 1.46 from yum install in /usr/include/boost or /usr/lib64)
  Manual install procedure
  
  1. I needed in some cases to first install python-dev and libbz2-dev
  2. $ sudo yum remove boost
  3. $ cd /programinstallers
  4. $ wget -N http://sourceforge.net/projects/boost/files/boost/1.54.0/boost_1_54_0.tar.gz
  5. $ tar -zxvf boost_1_54_0.tar.gz
  6. $ cd boost_1_54_0
  7. $ ./bootstrap.sh --prefix=/usr/local --libdir=/usr/local/lib64
  8. $ ./b2
  9. $ sudo ./b2 install
     

     Performing configuration checks
     
         - 32-bit                   : no
         - 64-bit                   : yes
         - arm                      : no
         - mips1                    : no
         - power                    : no
         - sparc                    : no
         - x86                      : yes
     error: No best alternative for libs/coroutine/build/allocator_sources
         next alternative: required properties: static windows multi
             not matched
         next alternative: required properties: static on multi
             not matched
         next alternative: required properties: static multi
             not matched
         - has_icu builds           : no
     warning: Graph library does not contain MPI-based parallel components.
     note: to enable them, add "using mpi ;" to your user-config.jam
         - zlib                     : yes
         - iconv (libc)             : yes
         - icu                      : no
         - icu (lib64)              : no
         - compiler-supports-ssse3  : yes
         - compiler-supports-avx2   : no
         - gcc visibility           : yes
         - long double support      : yes
     warning: skipping optional Message Passing Interface (MPI) library.
     note: to enable MPI support, add "using mpi ;" to user-config.jam.
     note: to suppress this message, pass "--without-mpi" to bjam.
     note: otherwise, you can safely ignore this message.
     error: No best alternative for libs/coroutine/build/allocator_sources
         next alternative: required properties: static windows multi
             not matched
         next alternative: required properties: static on multi
             not matched
         next alternative: required properties: static multi
             not matched
         - zlib                     : yes
     
     Component configuration:
     
         - atomic                   : building
         - chrono                   : building
         - context                  : building
         - coroutine                : building
         - date_time                : building
         - exception                : building
         - filesystem               : building
         - graph                    : building
         - graph_parallel           : building
         - iostreams                : building
         - locale                   : building
         - log                      : building
         - math                     : building
         - mpi                      : building
         - program_options          : building
         - python                   : building
         - random                   : building
         - regex                    : building
         - serialization            : building
         - signals                  : building
         - system                   : building
         - test                     : building
         - thread                   : building
         - timer                    : building
         - wave                     : building
     ...
     common.copy /usr/local/lib64/libboost_wave.a
     ...updated 11625 targets...

     
     This installed to /usr/local/include/boost and /usr/local/lib64

Installation

1. $ cd /programinstallers/
2. $ git clone --recursive https://github.com/genome/breakdancer.git
3. $ cd breakdancer
4. $ export SAMTOOLS_ROOT=/usr/lib/samtools/
5. $ export BOOST_LIBRARYDIR=/usr/local/lib64
6. $ export BOOST_INCLUDEDIR=/usr/local/include
7. $ export BOOST_ROOT=
8. $ export BOOST_ADDITIONAL_VERSIONS="1.54 1.54.0"
9. I don't know if this was actually necessary
   $ sudo ln -s /usr/local/include/boost /usr/local/include/boost/lib
10. $ cmake . -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local -DBoost_DEBUG=1
11. $ make
12. If necessary: Need to add location of 1.54 boost libraries to LD_LIBRARY_PATH
    $ sudo nano /etc/profile
    ...
    export LD_LIBRARY_PATH="/usr/local/lib64:$LD_LIBRARY_PATH"
    ...
13. Test and print version
    $ bin/breakdancer-max
14. Install
    $ cp -puv bin/breakdancer-max /usr/local/bin/
15. There was no BreakDancer-Mini in this version
16. $ cp -puv perl/*pm /usr/share/perl5/Local/
    

    `breakdancer/perl/AlnParser.pm' -> `/usr/share/perl5/Local/AlnParser.pm'
    `breakdancer/perl/Poisson.pm' -> `/usr/share/perl5/Local/Poisson.pm'

17. $ cp -puv perl/bam2cfg.pl /usr/local/bin/
    

    `breakdancer/perl/bam2cfg.pl' -> `/usr/local/bin/bam2cfg.pl'

18. Add this line to /usr/local/bin/bam2cfg.pl
    use lib '/usr/share/perl5/Local/';
19. For documentation web page:
    $ mkdir ../web/breakdancer
20. $ cp -puv README ../web/breakdancer/README.txt
21. Cleanup
    $ cd /programinstallers ; rm breakdancer -rf