ABySS

ABySS is a denovo assembler of short read data.

installing

I used the following script to install abyss in my home folder (/home/rov). I first had to install sparsehash and boost libraries.

   
#/bin/sh

#make and install abyss in my local directory
#cd into abyss source distribution dir
#and run this script using ../build_abyss.sh

load module openmpi

MYDIR="/ibers/ernie/home/rov/programs"

#boost does not need to be compiled
RJVBOOST="--with-boost=${MYDIR}/boost_1_54_0"

#found using find / 2> /dev/null | grep openmpi
RJVOPENMPI="--with-mpi=/cm/shared/apps/openmpi/gcc/64/1.4.4"

#see https://groups.google.com/forum/#!msg/abyss-users/6NXwP959RTI/tqLtO14a4A8J
RJVLDFLAGS="LDFLAGS=-L/cm/shared/apps/openmpi/gcc/64/1.4.4/lib64"

#probably only one of these required
RJVCPPFLAGS="-I${MYDIR}/sparsehash-2.0.2/src/google/sparsehash -I${MYDIR}/sparsehash-2.0.2/src/google -I${MYDIR}/sparsehash-2.0.2/src"

#where to put abyss binaries
RJVINSTALL="--prefix=${MYDIR}/abyss-local"

#ensure max kmer size is > 64
RJVMAXK='--enable-maxk=96'

./configure ${RJVINSTALL} ${RJVBOOST} ${RJVOPENMPI} ${RJVMAXK} ${RJVLDFLAGS} CPPFLAGS="${RJVCPPFLAGS}"
make
make install