Carrot root and DNA VCRU Bioinformatics USDA ARS Vegetable Crops Research Unit

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Installation notes for ABySS version 1.5.1 - May 8, 2014

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Prerequisites

Installation

  1. $ cd /programinstallers/
  2. $ ver="1.5.1"
  3. $ wget -N https://github.com/bcgsc/abyss/releases/download/$ver/abyss-$ver.tar.gz
  4. $ tar -zxvf abyss-$ver.tar.gz
  5. $ cd abyss-$ver
  6. Prepare install directory
    $ mkdir /usr/local/bin/abyss-$ver
  7. Indicate where Boost libraries are located
    $ ln -s /usr/include/boost boost
    or
    $ ln -s ../boost_1_55_0/boost boost
  8. Unless upgrading, indicate where openmpi is located
  9. Configure
  10. Make sure mpi works by checking for this in the log
    $ grep mpi configure.log
    ...
    checking mpi.h usability... yes
    checking mpi.h presence... yes
    checking for mpi.h... yes
    checking for MPI_Init in -lmpi... yes
    ...
    checking google/sparse_hash_map usability... yes
    ...
  11. The compiler flag -Wno-unused-local-typedefs fixed boost problem with newer gcc compilers, e.g. error: typedef 'boost_concept_check99' locally defined but not used [-Werror=unused-local-typedefs]
    $ make CXXFLAGS='-Wno-unused-local-typedefs'
  12. To confirm success, make sure ABYSS-P is in the Parallel directory
    $ ls Parallel
  13. Install
    $ make install
  14. If upgrading, remove old symlink
    $ rm /usr/local/bin/abyss
  15. Make a version-independent symlink
    $ ln -s /usr/local/bin/abyss-$ver /usr/local/bin/abyss
  16. Unless upgrading, add to default PATH
    $ sudo nano /etc/profile
    ...
    PATH="$PATH:/usr/local/bin/abyss/bin"
    PATH="$PATH:/usr/lib64/openmpi/bin" ← Fedora only
    ...
  17. Cleanup. Can remove the /programinstallers/boost_1_55_0b1 and /programinstallers/abyss-$ver directories