Software on M3

M3 uses a modular system to manage software.

Modules

Modules is software installed on M3 that provides an easy mechanism for updating your environment variables, so that your environment uses the correct version of software and libraries installed on M3.

Installed software modules

------------------------ /usr/share/Modules/modulefiles ------------------------
dot         module-git  module-info modules     null        use.own

------------------------ /usr/local/Modules/modulefiles ------------------------
3daprecon/0.0.1
3depict/0.0.15
3dslicer/4.6.0
3dslicer/4.8.1
abaqus/6.14
abyss/2.0.2
adxv/1.9.12
afni/16.2.16
afni/17.0.11
amber/18-multi-gpus
amber/18-parallel
amber/18-serial
amber/18-single-gpu
amira/6.3.0
anaconda/4.3.1-Python3.5
anaconda/4.3.1-Python3.5-gcc5
anaconda/5.0.1-Python2.7-gcc5
anaconda/5.0.1-Python3.5-gcc5
anaconda/5.0.1-Python3.6-gcc5
anaconda/5.1.0-Python3.6-gcc5
analyze/12.0
ansys/18.1
ants/1.9.v4
ants/2.2.0
arpack/2.1
arpack/3.1.3-2
ascp/3.5.4
atlas/3.10.2-gcc4
atlas/3.10.2-gcc5
atomprobedevcode/1.0.0(default)
attr/2.4.46-12
autodock_vina/1.1.2
avizo/9.0.1
avizo/9.3.0
avizo/9.3.0.1
avizo/9.4.0
axel/2.12
bamtools/2.4.1
bcbtoolkit/4.0.0
bcftools/1.6
bcftools/1.7
bcl2fastq/2.19.1
beagle/2.1.2
beast1/1.10.0
beast1/1.8.4
beast2/2.4.7
bedtools/2.26.0
bigdatascript/v0.99999e
biscuit/0.2.2
bismark/v0.19.1
blas/3.8.0-gcc5
boost/1.58.0
boost/1.62.0
boost/1.62.0-gcc4
boost/1.67.0-gcc5
bowtie/1.1.2
bowtie2/2.2.9
bsoft/1.9.2
bsoft/2.0(default)
buster/20170508
bwa/0.7.12
bzip2/1.0.6
caffe/1.0.0
caffe/1.0.0-protbuf32
caffe/caffe-matlab
caffe/caffe-tsn
caffe/deepvistool
caffe/latest(default)
caffe/rc4
caffe2/0.8.1
canu/1.7.1
caret/5.65
caw/0.2.4(default)
cblas/20032302-gcc5
ccp4/7.0
ccp4/ccp4i
ccp4/ccp4i2
ccp4/ccp4mg
ccp4/coot
cellprofiler/2.2.0
cellprofileranalyst/2.2.0
cellranger/2.0.1
chimera/1.10.2
chimera/1.11
chrome/default
cistem/1.0.0-beta
cloudstor/2.3.1-1.1
cmake/3.10.2-gcc4
cmake/3.10.2-gcc4-system
cmake/3.10.2-gcc5
cmake/3.5.2
cmake/3.5.2-gcc4
cmake/3.5.2-gcc5
comsol/5.2a
connectome/1.2.3
convert3d/1.0.0
coventormp/1.002
cplex/12.8.0
cpmd/3.17.1
cryosparc/beta
crystallography/0.0.3(default)
cst/2017
ctffind/4.0.17
ctffind/4.1.10
ctffind/4.1.3
ctffind/4.1.4
ctffind/4.1.8
cuda/4.1
cuda/6.0
cuda/7.0
cuda/7.5
cuda/8.0
cuda/8.0.61
cuda/8.0-DL
cudnn/5.1
cudnn/5.1-DL
cudnn/7.1.2-cuda8
cufflinks/2.2.1
cutadapt/0.16
cytoscape/3.4.0
daris-utils/1.0
deep-complex-networks/2017
deepmedic/0.6.1
detectron/20180322
dials/1.5.1
dicomnifti/2.32.1
dmtcp/2.5.2
dos2unix/7.4.0
drishti/2.6.3
drmaa/1.0.7
dti-tk/2.3.1
dtk/0.6.4.1
dynamo/1.1.178
eclipse/4.7.3a
effoff/0.2.1(default)
eigen/3.2.9
eigen/3.3.0
eiger2cbf/1.0
eman/2.12
eman/2.2
emapaccess/1.0(default)
emap-galaxy-shortcut/1.0.0(default)
emap-mytardis-shortcut/1.0.0(default)
emap-wiki-shortcut/0.0.1(default)
emspring/spring_v0-84-1470
emspring/spring_v0-84-1470_mlx
fastqc/0.11.7
fasttree/2.1.10
fastx-toolkit/0.0.13
fcsalyzer/0.9.12
feedback/1.0.1(default)
ffmpeg/3.4.2
fftw/3.3.4-gcc
fftw/3.3.5-gcc
fftw/3.3.5-gcc5
figtree/1.4.3
fiji/20160808
fiji/20170223
fiji/current
fiji/MMI-MHTP
fix/1.064
flexbar/3.4.0
fmriprep/1.0.15
fmriprep/1.1.1
fouriertransform/0.2.3(default)
freesurfer/20160922
freesurfer/5.3
freesurfer/6.0
freesurfer/devel-20171013
freesurfer/devel-20180612
fsl/5.0.11
fsl/5.0.9
fsleyes/0.22.4
fsleyes/0.23.0
gamess/16srs1
gap/4.8.10
gatk/3.4
gatk/3.7
gatk/4.0.1.1
gaussian/g16a03
gautomatch/0.53
gautomatch/0.56
gcc/4.9.3
gcc/5.4.0
gcc/6.1.0
gcc/8.1.0
gctf/0.50
gctf/0.66
gctf/1.06
gctf/1.06_cuda8
gctf/1.08_cuda8
gctf/1.18
gdcm/2.6.6-gcc4
gdcm/2.6.6-gcc5
geant4/10.02.p03
geant4/10.03.p01
geos/3.6
gflags/master
gflags/master-gcc4
gimp/2.8
gingerale/2.3.6
git/2.8.1
glew/2.0-gcc4
glew/2.0-gcc5
glog/master
glog/master-gcc4
glpk/4.60
gmp/6.1.2
gmsh/3.0.3
gnuparallel/20160822
gnuplot/5.2.1
gpu_burn/0.9
gpucomputingsdk/4.0.17
graphviz/2.30.1
gromacs/2016.3-openmpi-cuda8.0
gromacs/2016.4-openmpi-cuda8.0
gromacs/2018-openmpi-cuda8.0
gromacs/2018-openmpi-cuda8.0-NVML(default)
gsl/2.2-gcc4(default)
gsl/2.2-gcc5
gst-devel/1.4.5
gst-libav/1.10.4
gst-libav/1.4.5
gurobi/7.5.1
h5toxds/1.1.0
hdf5/1.10.0-patch1
htop/2.0.1
htseq/0.10.0
htslib/1.7
huygens/16.10.1-p1
icm/3.7-3b
icm/3.8.7
idl/8.6
igv/2.3.81
ihrsr++/v1.5
ilastik/1.2.0
imagemagick/7.0.5-7
imagescope/11.2.0.780
imod/4.8.54
imod-raza/4.7.12
imosflm/7.2.1
impute2/2.3.1
intel/2015.0.090
intel/2016
intel/2017u4
iqtree/1.5.3
iqtree/1.6.2
itk/4.10.0-gcc4
itk/4.10.0-gcc5
itk/4.8.2-gcc4
itk/4.8.2-gcc5
itksnap/3.3.x(default)
jags/3.3.0
jags/3.4.0
jags/4.3.0
java/1.7.0_67
java/1.8.0_77
jdk/10-20180320
jspr/2017-7-20
kallisto/0.43.0
kilosort/1.0
lammps/20180510(default)
lammps/nil
lapack/3.6.1-gcc4
lapack/3.6.1-gcc4-opt
lapack/3.6.1-gcc5
lapack/3.8.0-gcc5
leveldb/master
leveldb/master-gcc4
levelset/0.0.2(default)
libint/1.1.4
libjpeg-turbo/1.4.2
libjpeg-turbo/1.5.1
libsmm/20150702
libtiff/3.9.7
libxsmm/1.9
lmdb/latest
macs2/2.1.1.20160309
mafft/7.310
magma/1.6.1
magma/2.0.2
mango/4.0.1
mantid/3.8.0
mantid/3.9.0
mathematica/11.0.1
mathgl/1.11.2
mathgl/2.0.3(default)
matlab/r2015b
matlab/r2016a
matlab/r2017a
matlab/r2017b
matlab/r2017b-caffe
matlab/r2018a
maven/3.3.9
merantk/1.2.1
mesa/13.0.5
mesa/default
meshlab/2016.12-gcc5
mevislab/2.8.1-gcc-64bit
miakat/4.2.6
minc-lib/2.2-git-gcc4
miniconda3/4.1.11-python3.5
mne/TF-201804
motioncor2/2.1
motioncor2/2.1.10-cuda8
motioncorr/2.1
motioncorr2/20160822
mpfr/3.1.5
mpifileutils/20170922
mrbayes/3.2.6
mrf/0.2.2(default)
mricrogl/1.0.20170207
mricron/06.2013
mricron/30apr2016
mriqc/0.9.7
mrtrix/0.3.15-gcc4
mrtrix/0.3.15-gcc5
mrtrix/0.3.16
mrtrix/20170712
muscle/3.8.31
mxtools/0.1
mytardis/0.1(default)
namd/2.12-ibverbs-smp-cuda
namd/2.12-multicore
nanofilt/201807
nccl/master
nccl/master-gcc4
netcdf/4.4.1.1
neuro_workflow/2017v2
niftilib/2.0.0
niistat/9.oct.2016
nis-elements-viewer/4.20
nn/0.2.4(default)
novactf/03.2018
objexport/0.0.4(default)
opencv/3.4.1
opencv/3.4.1-gcc4
openfoam/4.1
openfoam/5.x
openmpi/1.10.3-gcc4-mlx
openmpi/1.10.3-gcc4-mlx-cuda75
openmpi/1.10.3-gcc4-mlx-verbs
openmpi/1.10.3-gcc4-mlx-verbs-cuda75
openmpi/1.10.3-gcc5
openmpi/1.10.3-gcc5-mlx
openmpi/1.10.7-intel
openmpi/1.10.7-mlx(default)
orca/4.0.1
paml/4.9
pbzip2/1.1.13
peakseq/1.3.1
perl/5.24.0
phenix/1.11.1
phyml/3.1
picard/2.9.2
pigz/2.3.3
pigz/2.3.4
plink/1.7
plink/1.9
pointless/1.10.28
posgen/0.0.1(default)
posminus/0.2.3(default)
protobuf/master
protobuf/master-gcc4
psi4/v1.1
pv/1.6.6
pyem/v0.1
pyem/v0.1-201806
pymol/1.8.2.1
pymol/1.8.6
python/2.7.11-gcc
python/2.7.12-gcc4(default)
python/2.7.12-gcc5
python/3.5.2-gcc
python/3.5.2-gcc4
python/3.5.2-gcc5
python/3.6.2
pyxnat/20170308
qatools/1.2
qiime2/2017.9
qiime2/2018.2
qiime2/2018.4
qt/5.7.1-gcc5
quit/1.1
R/3.3.1
R/3.4.3
R/3.5.0
raxml/8.2.9
rdf-kd/0.0.1(default)
relion/1.4
relion/2.02
relion/2.0.6
relion/2.0beta
relion/2.1(default)
relion/2.1.b1
relion/2.1.b2
relion/2.1-openmpi-1.10.7-mlx
resmap/1.1.4
resmap/1.1.5
resmap/1.9.5
rest/1.8
rest/1.8-matlab2017a.r6685
rings/1.3.3
r-launcher/0.0.1(default)
root/5.34.32
rosetta/2018.09
rsem/1.3.0
rstudio/1.0.143
rstudio/1.0.44
rstudio/1.1.414
rstudioserver_epigenetics/1.0
rstudioserver_epigenetics/1.0-20171101
samtools/1.3.1
samtools/1.6
samtools/1.7
sbt/0.13.15
scalapack/2.0.2
scipion/devel
scipion/devel-20170327
scipion/v1.0.1_2016-06-30
scipion/v1.1
scipion/v1.1.1
scipion/v1.2
scipion/v1.2.1
sdm_1d_calculate/2.0.2(default)
sdm_1d_plot/0.0.4(default)
sdm_2d_calculate/2.0.2(default)
sdm_2d_plot/0.0.4(default)
shapeit/v2_r837
simnibs/2.0.1g
simple/2.1
simple/2.5
singularity/2.2
singularity/2.3.1
singularity/2.4
singularity/2.4.2
singularity/2.4.5
singularity/2.5.1
singularity/c840a691d772c5a9d3981176ff3a1b849c6221c8
singularity/d3d0f3fdc4390c7e14a6065543fc85dd69ba42b7
singularity/dc816fa86ac79a6f20a1b1e8592a571498148825
skewer/20170212
smux/0.0.1
snappy/master
snappy/master-gcc4
snpm/13
soapdenovo2/2.04-r241
sourcetracker/2.0.1
sparsehash/2.0.3
spider/21.11
spm12/matlab2015b.r6685
spm8/matlab2015b.r6685
spm8/matlab2017a.r6685
squashfs-tools/4.3-0.21
sra-tools/2.7.0
star/2.5.2b
stata/14
strelka/2.8.4
structure/2.3.4
subread/1.5.1
surfice/7_feb_2017
synopsys/3.1(default)
tannertools/2016.1
tannertools/2016.2
tapsim/v1.0b_r766
tbb/20180312oss
tempest/1.5
tensorflow/1.0.0-python2.7.12-gcc5
tensorflow/1.3.0-python2.7.12-gcc5
tensorflow/1.4.0-python2.7.12-gcc5
tensorflow/1.4.0-python3.6-gcc5
terastitcher/20171106
texlive/2017
tiff/4.0.8
tigervnc/1.8.0
tmap/3.0.1
tophat/2.1.1
tracer/1.6
trackvis/0.6.1
trim_galore/0.4.5
trimmomatic/0.38
turbovnc/2.0.2(default)
turbovnc/2.1.0
ucsc-genome-tools/201806
unblur/1.0.2
unrar/5.0
valgrind/3.13
varscan/2.3.9
vasp/5.4.4
vep/90
vim/8.0.0596
virtualgl/2.5.0(default)
virtualgl/2.5.2
visit/2.12.3
vmd/1.9.3
voro++/0.4.6
vt/0.57
vtk/7.0.0
vtk/7.0.0-gcc5
wfu_pickatlas/3.0.5b
workspace/4.0.2
wxgtk/3.0.2
wxwidgets/3.0.3
xds/20170302
xds/monash(default)
xds/mxbeamteam
xjview/9.0
xjview/9.6
xnat-desktop/0.96
xnat-utils/0.2.1
xnat-utils/0.2.5
xnat-utils/0.2.6
xvfb/1.19.3
yade/1.20.0-cpu
yade/1.20.0-gpu
yasm/1.2.0-4
zetastitcher/0.3.3

Requesting an install

If you require additional software please email help@massive.org.au with the following details:

  • software
  • version
  • URL for download
  • urgency
  • if there are any licensing restrictions we need to impose

Docker based work flows

Many fields are beginning to distribute fully self contained pieces of software in a container format known as docker. Unfortunately docker is unsuited as a container format for shared user systems, however it is relatively easy to convert most docker containers for scientific work flows to the Singularity format. If you wish to run software based on a Docker container, please email help@massive.org.au and let us know where we can obtain the container and we will be happy to convert it for you.

Running QIIME on M3

QIIME (Quantitative Insights Into Microbial Ecology) 2 is installed on M3. To use this software:

 # Loading module
 module load qiime2/2017.9

# Unloading module
 module unload qiime2/2017.9

If you encounter issues with this install, please contact help@massive.org.au