ABySS

ABySS is a denovo assembler of short read data.

#/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