Introduction

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

Source: http://www.bcgsc.ca/platform/bioinfo/software/abyss

Module Usage

module load bioinformatics/abyss/1.3.3-openmpi

module display bioinformatics/abyss/1.3.3-openmpi
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/abyss/1.3.3-openmpi:

module-whatis    adds abyss directories to PATH etc.
Remember to add the following to your ~/.bashrc or ABYSS will not work between nodes

export ABYSS_LOADED_IN_SHELL=1
export OPENMPI_LOADED_IN_SHELL=1
module load bioinformatics/abyss/1.3.3-openmpi
setenv           OPENMPI_LOADED_IN_SHELL 1
prepend-path     PATH /sw/bioinformatics/abyss/1.3.3/openmpi/bin
prepend-path     MANPATH /sw/bioinformatics/abyss/1.3.3/openmpi/share/man
module           load boost/mpi/1.4.8-openmpi
module           load mpi/openMPI/1.4.3-gnu
module           load bioinformatics/sparsehash/2.0.2
-------------------------------------------------------------------

Installation

Dependencies
============

ABySS requires the following libraries:

ABySS requires a C++ compiler that supports
OpenMP(http://www.openmp.org) such as GCC(http://gcc.gnu.org).

module purge
module load boost/mpi/1.4.8-openmpi
module load mpi/openMPI/1.4.3-gnu
module load bioinformatics/sparsehash/2.0.2

cd /sw/bioinformatics/abyss/1.3.3/openmpi/src
tar -zxvf abyss-1.3.3.tar.gz
cd /sw/bioinformatics/abyss/1.3.3/openmpi/src


./configure --prefix=/sw/bioinformatics/abyss/1.3.3/openmpi --with-boost=/sw/library/boost/1.4.8/openmpi/include --with-mpi=/sw/openMPI/1.4.3-gnu/lib64 CPPFLAGS=-I/sw/bioinformatics/sparsehash/2.0.2/include 2>&1 | tee configure_abyss.txt

make 2>&1 | tee make_abyss.txt
make install 2>&1 | tee make_install_abyss.txt
Compiling ABySS from source
===========================

To compile and install ABySS in `/usr/local`:

        ./configure
        make
        sudo make install

To install ABySS in a specified directory:

        ./configure --prefix=/opt/abyss
        make
        sudo make install

ABySS uses OpenMP for parallelization, which requires a modern
compiler such as GCC 4.2 or greater. If you have an older compiler, it
is best to upgrade your compiler if possible. If you have multiple
versions of GCC installed, you can specify a different compiler:
 ./configure --with-boost=/usr/local/include
 ./configure --with-mpi=/usr/lib/openmpi

ABySS should be built using the sparsehash library to reduce memory
usage, although it will build without. sparsehash should be found in
`/usr/include` or its location specified to `configure`:

        ./configure CPPFLAGS=-I/usr/local/include

The default maximum k-mer size is 64 and may be decreased to reduce
memory usage or increased at compile time:

        ./configure --enable-maxk=96