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Applications Overview

Running HPC Applications

Typically, applications are configured as modules and can be loaded if required.

To setup your environment to use a package you need to enter:

module load <package>

Replacing <package> with the relevant module name, followed by the version number, if a version other than the default is required. More information about module commands is available here.

To request the installation of an application please enter the details on the application request page.

In order for an application to be installed on the cluster, we will need to be able to test the installation.
If you cannot provide a suitable set of tests, please contact us and we will work with you to arrange appropriate tests.

List of modules available on Apocrita

Application Versions Default
7zip 16.02 16.02
R 3.3.2, 3.4.0, 3.4.2, 3.4.3 3.4.3
abaqus 2016 2016
abyss 2.0.2 2.0.2
amber 16 16
angsd 0.919 0.919
ansys 18.0.0 18.0.0
arrayfire 3.4.2 3.4.2
asciinema 1.3.0, 1.4.0 1.4.0
aspell 0.60.6 0.60.6
aspera 3.7.2 3.7.2
atlas 3.10.3 3.10.3
augustus 3.2.3 3.2.3
autoconf-archive 2017.09.28 2017.09.28
bamtools 2.4.1 2.4.1
bcftools 1.4, 1.8 1.8
bcl2fastq2 2.19.1 2.19.1
bedtools 2.26.0 2.26.0
bismark 0.19.0 0.19.0
blast+ 2.6.0, 2.7.1 2.7.1
blat 35 35
blobtools 0.9.19.6 0.9.19.6
boost 1.63.0 1.63.0
bowtie 1.2.0 1.2.0
bowtie2 2.3.1, 2.3.2, 2.3.4 2.3.4
breakdancer 1.4.5 1.4.5
bucky 1.4.4 1.4.4
busco 3.0 3.0
bwa 0.7.15, 0.7.17 0.7.17
bwameth 0.2.0 0.2.0
canu 1.5, 1.6 1.5
clustalw 2.1 2.1
cmake 3.8.0 3.8.0
cp2k 4.1.0-intel, 5.1-openmpi-nxn, 4.1 5.1-openmpi-nxn
cuda 8.0.44, 9.2.88 8.0.44
cudnn 5.0-cuda8.0, 5.1-cuda8.0, 6.0-cuda8.0, 7.1-cuda-9.2 6.0-cuda8.0
cufflinks 2.2.1 2.2.1
dl_poly 4.08-openmpi, 4.08-openmpi-gcc-nxn, 4.08-openmpi-gcc-nxv, 4.08-plumed 4.08-openmpi
eigen 3.3.4 3.3.4
emboss 6.6.0 6.6.0
ensembl-vep 89.7 89.7
entrez 201708 201708
exomiser 7.2.3 7.2.3
exonerate 2.4.0 2.4.0
fastqc 0.11.5 0.11.5
ffmpeg 3.2.4, 3.3.3 3.3.3
fftw 3.3.6-pl1-intel, 3.3.6-pl2-gcc 3.3.6-pl1-intel
frc-align 1.3.0 1.3.0
freebayes 1.1.0 1.1.0
gamess 201704-R1 201704-R1
gaussian g09_D01, g16 g09_D01
gcc 6.3.0, 7.1.0 7.1.0
gdb 7.12 7.12
genometools 1.5.9 1.5.9
git 2.12.0 2.12.0
glfw 3.2.1 3.2.1
gnuplot 5.2.0 5.2.0
gromacs 5.1.4-gpu, 5.1.4-intelmpi, 2016.3-gpu, 2016.3-intelmpi, 2016.3-plumed 2016.3-intelmpi
gsl 2.4 2.4
guidance 2.02 2.02
gulp 5.0.1 5.0.1
hdf5-parallel 1.8.18-intel 1.8.18-intel
hmmer 3.1b2, 3.1b2-1 3.1b2-1
htop 2.0.2 2.0.2
htslib 1.4, 1.6, 1.8 1.8
hyphy 2.3.6 2.3.6
idl 8.4.1 8.4.1
imagemagick 7.0.5-4 7.0.5-4
intel 2017.1, 2017.3, 2018.1 2017.3
intelmpi 2017.1, 2017.3, 2018.1 2017.3
intelpython 2.7.12-2017.2, 3.5.2-2017.2, 2.7.12, 3.5.2 3.5.2-2017.2
java 1.8.0_121-oracle, 1.8.0_152-oracle, 9.0.1-oracle 1.8.0_152-oracle
jellyfish 2.2.6 2.2.6
jmodeltest2 2.1.10r20160303 2.1.10r20160303
julia 0.5.2, 0.5.2-1 0.5.2
kmc a09d63a4 a09d63a4
lammps 11AUG17-intelmpi 11AUG17-intelmpi
lapack 3.7.0 3.7.0
last 869 869
lastz 1.04.00 1.04.00
longranger 2.1.3, 2.1.4 2.1.4
mafft 7.310 7.310
maker 2.31.9-mpi, 2.31.9 2.31.9-mpi
masurca 3.2.2 3.2.2
mathematica 11.0.1 11.0.1
matlab 2016a, 2017a, 2018a 2017a
meerkat 0.189 0.189
metis 5.1.0 5.1.0
migrate 3.6.11 3.6.11
minimap2 2.5 2.5
mira 4.0.2 4.0.2
mopac2016 18.063 18.063
mothur 1.39.5 1.39.5
mrbayes 3.2.6-mpi 3.2.6-mpi
multisnv 2.3-12 2.3-12
muscle 3.8.31 3.8.31
namd 2.12-gpu, 2.12-openmpi 2.12-openmpi
nano 2.8.6 2.8.6
newick_utils 1.6 1.6
nextflow 0.25.7, 0.26.3 0.26.3
nwchem 6.6-mpi 6.6-mpi
octave 4.2.1 4.2.1
openbabel 2.4.1 2.4.1
openmpi 2.0.2-gcc, 2.1.0-gcc, 2.1.1-intel, 3.0.0-gcc 3.0.0-gcc
parallel 20170422 20170422
paraview 4.4.0, 5.3.0 5.3.0
perl 5.24.1, 5.26.0 5.26.0
pgi 17.10 17.10
phylobayes 4.1c 4.1c
phylobayes-mpi 01cbc7d 01cbc7d
plink 1.9-170906, 2.0-20170920 1.9-170906
plumed 2.4.0-intelmpi-nxv, 2.4.0-nxv, 2.4.0 2.4.0
prank 170427 170427
primer3 2.4.0 2.4.0
python 2.7.13, 2.7.13-1, 2.7.13-3, 2.7.14, 2.7.15, 3.6.1, 3.6.2, 3.6.2-2, 3.6.3 3.6.3
qe 6.1.0-mpi 6.1.0-mpi
qt 5.8.0 5.8.0
qualimap 2.2.1 2.2.1
quast 4.5-1, 4.6.1 4.6.1
raxml 8.2.11 8.2.11
repeatmasker 4.0.7 4.0.7
ruby 2.4.1 2.4.1
samtools 0.1.19, 1.4, 1.4.1, 1.6, 1.8 1.8
scalapack 2.0.2-intel 2.0.2-intel
scilab 6.0.0 6.0.0
seqtk 1.2 1.2
shengbte 1.1.1 1.1.1
singularity 2.5.1 2.5.1
smac3 0.8.0 0.8.0
soapdenovo2 r241 r241
spades 3.11.1 3.11.1
sparsehash 2.0.3 2.0.3
sratools 2.8.2-1 2.8.2-1
stacks 1.46 1.46
star 2.5.3a 2.5.3a
star-ccm+ 11.06.011-R8, 12.02.010, 12.02.010-R8 12.02.010-R8
stata 13, 15 13
swig 3.0.12 3.0.12
tbb 2018_U2 2018_U2
texinfo 4.8 4.8
tmux 2.7 2.7
tophat 2.1.1 2.1.1
transdecoder 5.0.2 5.0.2
trimgalore 0.4.5-1 0.4.5-1
trimmomatic 0.36 0.36
trinity 2.4.0 2.4.0
valgrind 3.12.0 3.12.0
vcftools 0.1.15 0.1.15
vmd 1.9.3 1.9.3
wise2 2.4.1 2.4.1
yasm 1.3.0 1.3.0
zsh 5.4.1, 5.4.2 5.4.2