Preduvjet za instalaciju jest instalacija biblioteke Google Sparsehash:
wget -c https://github.com/sparsehash/sparsehash/archive/sparsehash-2.0.3.tar.gz ./configure --prefix=/apps/sparsehash make && make install
Instalacija ABySS je obavljena kompajliranjem izvornog koda s Intel 2019 i OpenMPI 3.0:
module load mpi/openmpi3-intel-x86_64 ./configure CC=icc CXX=icpc CPPFLAGS=-I/usr/include/openmpi3-intel-x86_64 --with-mpi=/usr/lib64/openmpi3-intel/ --with-sparsehash=/apps/sparsehash203 --prefix=/apps/abyss214 --disable-openmp make && make install
Dostupne verzije su:
| Verzija | Modul |
|---|---|
| 2.1.4 | abyss/2.1.4 |
Primjer korištenja:
#!/bin/sh
#$ -N ABySS
#$ -q a16.q
#$ -pe *mpisingle 4
#$ -cwd
module load abyss/2.1.4
abyss-pe np=$NSLOTS name=$(basename ${1%.*}) k=96 in=${1} -se
Podnošenje posla
% qsub abyss.sge chr1_1.fa 96