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
Home Page
Prerequisites
- Google sparsehash
- $ cd /programinstallers
- $
wget -N http://sparsehash.googlecode.com/files/sparsehash_2.0.2-1_amd64.deb
- $
sudo dpkg -i sparsehash_2.0.2-1_amd64.deb
- $ sudo apt-get install libsparsehash-dev
- Boost C++ Libraries
Either
- $ sudo apt-get install libboost-all-dev
or
- $ cd /programinstallers/
- $ wget -N http://downloads.sourceforge.net/project/boost/boost/1.55.0/boost_1_55_0.tar.gz
- $ tar -zxvf boost_1_55_0.tar.gz
- OpenMPI
- Fedora: $ sudo yum install openmpi openmpi-devel
Ubuntu: $ sudo apt-get install openmpi-bin openmpi-doc libopenmpi-dev
- ghc
- $ sudo apt-get install ghc
- sqlite3
- $ sudo apt-get install libsqlite3-dev
Installation
- $ cd /programinstallers/
- $ ver="1.5.1"
- $ wget -N https://github.com/bcgsc/abyss/releases/download/$ver/abyss-$ver.tar.gz
- $ tar -zxvf abyss-$ver.tar.gz
- $ cd abyss-$ver
- Prepare install directory
$ mkdir /usr/local/bin/abyss-$ver
- Indicate where Boost libraries are located
$ ln -s /usr/include/boost boost
or
$ ln -s ../boost_1_55_0/boost boost
- 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
- 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
- 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
...
- 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'
- To confirm success, make sure ABYSS-P is in the Parallel directory
$ ls Parallel
- Install
$ make install
- If upgrading, remove old symlink
$ rm /usr/local/bin/abyss
- Make a version-independent symlink
$ ln -s /usr/local/bin/abyss-$ver /usr/local/bin/abyss
- 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
...
- Cleanup. Can remove the /programinstallers/boost_1_55_0b1 and /programinstallers/abyss-$ver directories