This page was last updated on Friday, 15-Nov-2019 09:02:52 CST

Installation notes for ABySS version 1.5.1 - May 8, 2014

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Prerequisites

• Google sparsehash
  1. $ cd /programinstallers
  2. $ wget -N http://sparsehash.googlecode.com/files/sparsehash_2.0.2-1_amd64.deb
  3. $ sudo dpkg -i sparsehash_2.0.2-1_amd64.deb
  4. $ sudo apt-get install libsparsehash-dev
• Boost C++ Libraries
  Either
  1. $ sudo apt-get install libboost-all-dev
  or
  1. $ cd /programinstallers/
  2. $ wget -N http://downloads.sourceforge.net/project/boost/boost/1.55.0/boost_1_55_0.tar.gz
  3. $ tar -zxvf boost_1_55_0.tar.gz
• OpenMPI
  1. Fedora: $ sudo yum install openmpi openmpi-devel
     Ubuntu: $ sudo apt-get install openmpi-bin openmpi-doc libopenmpi-dev
• ghc
  1. $ sudo apt-get install ghc
• sqlite3
  1. $ sudo apt-get install libsqlite3-dev

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
   • Fedora
     $ sudo ln -s /usr/include/openmpi-x86_64 /etc/openmpi-x86_64/include
     $ sudo ln -s /usr/lib64/openmpi/lib /etc/openmpi-x86_64/lib
   • Ubuntu 12.04 (this was not needed for 13.10, 14.04)
     $ sudo ln -s /usr/lib/openmpi/include /etc/openmpi/include
     $ sudo ln -s /usr/lib/openmpi/lib/ /etc/openmpi/lib
9. Configure
   • Fedora
     $ ./configure --prefix=/usr/local/bin/abyss-$ver --with-mpi=/etc/openmpi-x86_64 --enable-maxk=96 --with-sqlite=/usr/local/lib64/R/library/RSQLite/include/ fail > configure.log
   • Ubuntu
     $ ./configure --prefix=/usr/local/bin/abyss-$ver --with-mpi=/etc/openmpi --enable-maxk=96 > configure.log
   • Ubuntu 13.10, 14.04, 16.04
     $ ./configure --prefix=/usr/local/bin/abyss-$ver --with-mpi=/usr/lib/openmpi --enable-maxk=96 > configure.log
   • Ubuntu 18.04
     $ ./configure --prefix=/usr/local/bin/abyss-$ver --with-mpi=/usr/lib/x86_64-linux-gnu/openmpi --enable-maxk=96 > configure.log
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