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

Jump to software beginning with A B C D E F G H I J K L M N O P Q R S T U V W X Y Z.

Attention

Some software packages on M3 have license conditions that restrict access to the software to certain user groups. These software packages are marked with the restricted keyword. To apply for access to restricted software, log in to the HPC ID system and navigate to the Software section of your profile. To enquire about restricted software contact the MASSIVE Help Desk

Note

The Monash Bioinformatics Platform (MBP) maintains a software stack on M3. More information, including how to access this software stack, can be found on the Bioinformatics community page.

Software

Version(s)

3daprecon restricted

0.0.1, 1.0

3depict restricted

0.0.15

3dslicer

4.6.0, 4.8.1

A

abaqus restricted

6.14

abinit

8.8.3

abricate

0.8.13

abyss

2.0.2

adxv

1.9.12

afni

16.2.16, 17.0.11

align2rawsignal

2.0

amber restricted

18-multi-gpus, 18-parallel, 18-serial, 18-single-gpu

amira restricted

6.3.0, 6.4.0, 6.5.0

anaconda

2018.12-Python3.7-gcc6, 2019.03-Python3.7-gcc5, 4.3.1-Python3.5, 4.3.1-Python3.5-gcc5, 5.0.1-Python2.7-gcc5, 5.0.1-Python3.5-gcc5, 5.0.1-Python3.6-gcc5, 5.1.0-Python3.6-gcc5

analyze restricted

12.0

ansys restricted

18.1, 19.1

ants

1.9.v4, 2.2.0

apex

latest

apr

1.6.5

apr-util

1.6.1

argos

3.0.0-beta52

ariba

2.12.1

armadillo

9.200-rc1

arpack

2.1, 3.1.3-2

ascp

3.5.4

atlas

3.10.2-gcc4, 3.10.2-gcc5

atomprobedevcode restricted

1.0.0(default)

attr

2.4.46-12

autodock_vina

1.1.2

avizo restricted

9.0.1, 9.3.0, 9.3.0.1, 9.4.0, 9.5.0, 9.7

axel

2.12

B

bamtools

2.4.1

barrnap

0.9

bart

0.4.04

bayenv

2.0

bayesass

1.3, 3.04

bbcp

17.12

bcbtoolkit

4.0.0

bcftools

1.6, 1.7, 1.8

bcl2fastq

2.19.1

beagle

2.1.2

beast1

1.10.0, 1.8.4

beast2

2.4.7, 2.4.8, 2.5.0

bedtools

2.26.0, 2.26.0-gcc5, 2.27.1-gcc5

bids-validator

2019.01

bigdatascript

v0.99999e

bigwigtowig

377-0

biscuit

0.2.2, 0.3.8.20180515

bismark

v0.19.1

bison

2.7.1

blas

3.8.0-gcc5, 3.8.0-gcc5-pic

blast

2.2.30, 2.3.0, 2.7.1(default)

boost

1.46.0-gcc5, 1.46.1-gcc5, 1.52.0-gcc5, 1.58.0, 1.58.0-gcc5, 1.62.0, 1.62.0-gcc4, 1.67.0-gcc5

bowtie

1.1.2

bowtie2

2.2.9, 2.3.5

brain_age

v1.0_18Jan2018

breseq

0.29.0, 0.33.2

bsoft

1.9.2, 2.0(default)

buster

20170508

bwa

0.7.12, 0.7.17-gcc5

bzip2

1.0.6

C

caffe

1.0.0, 1.0.0-protbuf32, caffe-matlab, caffe-tsn, deepvistool, latest(default), rc4

caffe2

0.8.1

caffe_enet

1.0

caffe_unet

1.0, 2.0

canu

1.7.1

caret

5.65

caw restricted

0.2.4(default)

cblas

20032302-gcc5

ccp-em

1.3.0

ccp4

7.0, 7.0.072, ccp4i, ccp4i2, ccp4mg, coot

cdhit

4.8.1

cellprofiler

2.2.0, 3.1.5

cellprofileranalyst

2.2.0

cellranger

2.0.1, 3.0.2

centrifuge

1.0.4-beta

chimera

1.10.2, 1.11, 1.13

chimerax

0.6, 0.8

chrome

68, 69, default

circos

0.69-6

cistem

1.0.0-beta

clamms

1.1

clonalframeml

1.11

cloudstor

2.3.1-1.1, 2.4.1, 2.4.2

cmake

2.8.12.2, 2.8.12.2-gcc5, 3.10.2-gcc4, 3.10.2-gcc4-system, 3.10.2-gcc5, 3.5.2, 3.5.2-gcc4, 3.5.2-gcc5

cmkl

9.1.023

cnvkit

0.9.5

comsol restricted

5.2a, 5.4

connectome

1.2.3

convert3d

1.0.0

coventormp

1.002

cp2k

6.1.0

cplex restricted

12.6, 12.6.3, 12.7.1, 12.8.0

cpmd

3.17.1

crisprcasfinder

1.05

crispresso

1.0.13-gcc5

cryo-em-processing-tool

0.1

cryolo

1.0.0, 1.1.3, 1.3.1

cryosparc

beta, cryosparc-cluster, v2

crystallography restricted

0.0.3(default)

cst

2017

ctffind

4.0.17, 4.1.10, 4.1.13, 4.1.3, 4.1.4, 4.1.8

ctftilt

latest

cuda

10.0, 4.1, 4.1.bajk, 6.0, 7.0, 7.5, 8.0, 8.0.61, 8.0-DL, 9.0, 9.1

cudadeconv

1.0

cudalibs8to9

0.1

cudnn

5.1, 5.1-DL, 7.1.2-cuda8, 7.1.3-cuda9, 7.3.0-cuda9

cufflinks

2.2.1

cunit

2.1.3

cutadapt

0.16

cytoscape

3.4.0

D

daris-utils

1.0

darknet

alexey, darknet_yolo_v3, latest

dcmtk

3.6.3

deep-complex-networks

2017

deepmedic

0.6.1, 0.7.0

deeptools

3.1.2, 3.1.3

dense3dcrf

20160527

detectron

20180322

dials

1.12.1, 1.5.1

diamond

0.9.22

dicomnifti

2.32.1

diyabc

2.1.0

dmtcp

2.5.2

dos2unix

7.4.0

dragondisk

1.0.5

drishti

2.6.3, 2.6.4

drmaa

1.0.7, 1.1.0

dti-tk

2.3.1

dtk

0.6.4.1

dynamo

1.1.178

dynet

2.1-cpu, 2.1-gpu

E

ea-utils

1.1.2, 1.1.2-gcc5

eclipse

4.7.3a, 4.8

effoff restricted

0.2.1(default)

eigen

2.0.17, 3.2.9, 3.3.0

eigensoft

7.2.1

eiger2cbf

1.0

elf

1.0

eman

2.12, 2.2, 2.22, 2.3

emap-galaxy-shortcut

1.0.0(default)

emap-mytardis-shortcut

1.0.0(default)

emap-wiki-shortcut

0.0.1(default)

emapaccess

1.0(default)

emboss

6.6.0

emspring

spring_v0-84-1470, spring_v0-84-1470_mlx

exciting

nitrogen

exploredti

4.8.6

F

fastani

1.1

fastml

3.1

fastqc

0.11.7

fastQValidator

0.1.1a

fastspar

0.0.7

fasttree

2.1.10

fastx-toolkit

0.0.13

fcsalyzer

0.9.12

fdtd

8.21.1933

feedback

1.0.1(default)

ffmpeg

3.4.2

fftw

3.3.4-gcc, 3.3.5-gcc, 3.3.5-gcc5

fgbio

0.9.0

figtree

1.4.3

fiji

20160808, 20170223, 20170530, current, MMI-MHTP

fix

1.064, 1.068

flash

1.2.11-gcc5

flexbar

3.4.0

flye

2.3.5

fmriprep

1.0.15, 1.1.1, 1.2.5, 1.3.0_post2, 1.4.0

foma

0.9.18

fooof

0.1.3

fouriertransform restricted

0.2.3(default)

freebayes

0.9.9

freesurfer

20160922, 5.3, 6.0, 6.0-patch, devel-20171013, devel-20180612, devel-20190128

fsl restricted

5.0.11, 5.0.9, 6.0.0, 6.0.1

fsleyes

0.22.4, 0.23.0, 0.24.3

ftgl

2.1

G

gamess

16srs1, 16srs1-v2, 2018r3

gap

4.8.10

gatk

3.4, 3.7, 4.0.1.1, 4.0.11.0

gauss restricted

11.0, 9.0

gaussian restricted

g16a03

gautomatch

0.53, 0.56

gcat

e48bf8b

gcc

4.9.3, 5.4.0, 6.1.0, 8.1.0

gctf

0.50, 0.66, 1.06, 1.06_cuda8, 1.08_cuda8, 1.18, 1.18_b2, 1.18_b2_cuda9, 1.18_cuda8, 1.18_cuda91

gd-devel

2.0.35

gdal

2.2.4, 2.3.1

gdb

8.2.1

gdcm

2.6.6-gcc4, 2.6.6-gcc5

geant4

10.02.p03, 10.03.p01

gem

3.3

geos

3.6

gflags

master, master-gcc4

gimp

2.8, 2.8.22

gingerale

2.3.6

git

2.17.0, 2.19.0, 2.8.1

git-annex

6.20180227

glew

2.0-gcc4, 2.0-gcc5

glm

0.9.9.5

glog

master, master-gcc4

glpk

4.60

gmp

6.1.2

gmsh

3.0.3

gnuparallel

20160822, 20190122

gnuplot

5.2.1

go

1.11.1

goctf

1.1.0

gpu_burn

0.9, 1.0

gpucomputingsdk

4.0.17

graphviz

2.30.1

gromacs

2016.3-openmpi-cuda8.0, 2016.4-openmpi-cuda8.0, 2016.5-openmpi-cuda8.0-plumed, 2018.4-openmpi-cuda8.0, 2018-openmpi-cuda8.0, 2018-openmpi-cuda8.0-NVML(default), 5.1.4

gsl

1.15.13-system, 2.2-gcc4(default), 2.2-gcc5, 2.2-system, 2.5-gcc4

gst-devel

1.4.5

gst-libav

1.10.4, 1.4.5

gubbins

2.3.2

gurobi restricted

7.5.1, 8.0.0

gvcftools

0.17.0

H

h5toxds

1.1.0

hdf5

1.10.0-patch1

hdfview

3.0

hisat2

2.1.0

hmmer

2.4i, 3.2.1

hotspot

4.0.0

htop

2.0.1

htseq

0.10.0

htslib

1.7, 1.9, 1.9-gcc5

huygens

16.10.1-p1

hyperspy

1.4

hypre

2.11.2, 2.15.0

I

icm restricted

3.7-3b, 3.8.7

idl

8.6

idr

2.0.3

igv

2.3.81, 2.4.19

ihrsr++

v1.5

ilastik

1.2.0

illumina-utils

2.6, 2.6-python3.7

imagej

20160205

imagemagick

7.0.5-7, 7.0.8-23, 7.0.8.23-native

imagescope

11.2.0.780

imblproc

20190405

imod

4.8.54, 4.9.9

imod-raza

4.7.12

imosflm

7.2.1, 7.2.2

impute2

2.3.1

intel

2015.0.090, 2016, 2017u4, 2018test, 2018u3

iqtree

1.5.3, 1.6.10, 1.6.2

ismapper

2.0

itk

4.10.0-gcc4, 4.10.0-gcc5, 4.10.0-gcc5-p1, 4.13.0-gcc4, 4.13.1-gcc4, 4.8.2-gcc4, 4.8.2-gcc5

itksnap

3.3.x(default), 3.8.0-beta

J

jags

3.3.0, 3.4.0, 4.3.0

java

1.7.0_67, 1.8.0_77

jdk

10-20180320

jellyfish

1.1.12

jspr

2017-7-20

K

kallisto

0.43.0

kaptive

0.5.1

kilosort

1.0

king

2.1.6

kleborate

0.2.0, 0.3.0

kraken

1.1.1

kraken2

2.0.7-beta

L

lammps

20180510(default), 20181212

lapack

3.6.1-gcc4, 3.6.1-gcc4-opt, 3.6.1-gcc5, 3.8.0-gcc5, 3.8.0-gcc5-pic

ldmap

28apr15

leveldb

master, master-gcc4

levelset restricted

0.0.2(default)

libertem

20190521

libffi

3.2.1

libffi-devel

3.0.13

libgd

2.2.4

libgeotiff

1.4.2

libharu

2.2.1

libint

1.1.4

libjpeg-turbo

1.4.2, 1.5.1

libsmm

20150702

libtiff

3.9.7, 4.0.10

libuuid

2.23.2-43

libxc

4.1.0

libxsmm

1.9

libzip

0.10.1-8

lighter

1.1.2

lmdb

latest

lofreq

2.1.3.1

lsd

0.3beta

M

macs2

2.1.1.20160309

mafft

7.310

magma

1.6.1, 2.0.2

mango

4.0.1

manta

1.5.0-gcc5

mantid

3.13.0, 3.8.0, 3.9.0

mash

2.1(default), 2.1.1

materialsstudio

18.1.0

mathematica

11.0.1, 12.0.0

mathgl

1.11.2, 2.0.3(default), 2.3.3

matlab

r2012b, r2014a, r2015b, r2016a, r2017a, r2017b, r2017b-caffe, r2018a, r2019a

mauve

20150213

maven

3.3.9

maxquant

1.6.5.0

mc

4.8.21

mcl

11-294

mcr2010b

1.0

megahit

1.1.3, 1.2.4-beta

meme

5.0.1

merantk

1.2.1

mercurial

4.7.1

mesa

13.0.5, default

meshlab

2016.12-gcc5, 2019.03

metaplotr

2018_09

metawrap

1.1.3

mevislab

2.8.1-gcc-64bit

miakat restricted

4.2.6

minc-lib

2.2-git-gcc4

minc-tools

2.2

miniconda3

4.1.11-python3.5

minizinc

2

mixcr

3.0.7

mkl

2018u3

mlst

2.15

mne

TF-201804

molden

5.7

mono

5.20.1.19

moose

1.0

morphind

1.4

motioncor2

20180924, 20181020, 20181020-cuda91, 2.1, 2.1.10-cuda8, 2.1.10-cuda9.1

motioncorr

2.1

motioncorr2

20160822

mpfr

3.1.5

mpifileutils

20170922

mrbayes

3.2.6, 3.2.6-mpi

mrf restricted

0.2.2(default)

mriconvert

2.1.0

mricrogl

1.0.20170207

mricron

06.2013, 30apr2016

mriqc

0.14.2, 0.9.7

mrtrix

0.3.15-gcc4, 0.3.15-gcc5, 0.3.16, 20170712, 3.0_rc3

msm_hocr

3.0

mummer

3.23-gcc5, 4.0.0.beta2-gcc5

muscle

3.8.31

mustem

5.3

mxtools

0.1

mytardis

0.1(default)

N

namd

2.12-ibverbs-smp-cuda, 2.12-multicore, 2.13-multicore-CUDA

nanofilt

201807

nanopolish

0.10.1, 0.11.1

nccl

master, master-gcc4

netcdf

4.4.1.1(default), 4.4.1.1-openmpi-1.10.7-mlx

neuro_workflow

2017v2

newick-utils

1.6

ngsqctoolkit

2.3.3

niftilib

2.0.0

niistat

9.oct.2016

nis-elements-viewer

4.20

nn restricted

0.2.4(default)

novactf

03.2018

nullarbor

2.0.20181010

O

objexport restricted

0.0.4(default)

octopus

8.4

openblas

0.2.20

opencv

3.4.1, 3.4.1-gcc4

openfoam

4.1, 5.x

openjpeg

2.3.0

openmpi

1.10.3-gcc4-mlx, 1.10.3-gcc4-mlx-cuda75, 1.10.3-gcc4-mlx-verbs, 1.10.3-gcc4-mlx-verbs-cuda75, 1.10.3-gcc5, 1.10.3-gcc5-mlx, 1.10.7-1.mlx, 1.10.7-intel, 1.10.7-mlx(default)

opennmt-py

0.7.0

openrefine

3.1

orca

4.0.1

P

packer

1.3.5

paml

4.9

paraview

4.0.1, 5.6.0

pastml

1.0

pbzip2

1.1.13

peakseq

1.3.1

perl

5.24.0, 5.28.0

petsc

3.10.1-gcc5

pgi

19.4, 2019

phenix restricted

1.11.1, 1.15.1, 1.15.2

phreeqc

3.5.0

phyml

3.1

picard

2.19.0, 2.9.2

pigz

2.3.3, 2.3.4

pilon

1.22

pindel

0.6.3-gcc5

plink

1.7, 1.9

plinkseq

0.10

plumed

2.5.0

pmix

4.0.0, v2.2

pointless

1.10.28

posgen restricted

0.0.1(default)

posminus restricted

0.2.3(default)

prank

170427

prodigal

2.6.3

proj

4.9.3, 5.1.0

prokka

1.13.3

protobuf

master, master-gcc4

psi4

v1.1

pv

1.6.6

pycharm

2018.3.3

pydeface

1.1.0

pyem

v0.1, v0.1-201806, v0.3

pymol

1.8.2.1, 1.8.6, 2.4.0a0

pypy

7.0.0-3.6

python

2.7.11-gcc, 2.7.12-gcc4(default), 2.7.12-gcc5, 2.7.15-gcc5, 3.5.2-gcc, 3.5.2-gcc4, 3.5.2-gcc5, 3.6.2, 3.6.2-static, 3.6.6-gcc5, 3.7.2-gcc6, 3.7.3-system

pytorch

1.0-cuda10

pyxnat

20170308

Q

qatools

1.2

qhull

2003.1, 2015.2

qiaseq-dna

1.0

qiime1

1.9.1

qiime2

2017.9, 2018.11, 2018.2, 2018.4, 2019.1, 2019.4

qt

5.7.1-gcc5

qt5-qtwebkit

5.9.1

quicktree

2.0, 2.5

quit

1.1, 2.0.2

R

3.3.1, 3.4.3, 3.5.0, 3.5.1, 3.5.2-openblas, 3.5.3-mkl, 3.6.0-mkl

R

r-launcher

0.0.1(default)

racon

1.3.1

raxml

8.2.12, 8.2.9

razers3

3.5.8

rdf-kd restricted

0.0.1(default)

relion

1.4, 2.02, 2.0.6, 2.0beta, 2.1(default), 2.1.b1, 2.1.b2, 2.1-openmpi-1.10.7-mlx, 3.0-20181109-cuda80, 3.0-20181109-cuda91, 3.0-20190115, 3.0.5, 3.0.5-uow, 3.0.6, 3.0.6-uow, 3.0-beta, 3.0-stable, 3.0-stable-cuda91, 3.0-stable-uow, 3.0-uow-20180904, 3.0-uow-20180917, 3.0-uow-20181109-cuda80, 3.0-uow-20181109-cuda91, 3.0-uow-20190115

resmap

1.1.4, 1.1.5, 1.9.5

rest

1.8, 1.8-matlab2017a.r6685

rings

1.3.3

rnammer

1.2

roary

3.11.2(default), 3.12.0

root

5.34.32

rosetta restricted

2018.09

rsem

1.3.0

rstudio

1.0.143, 1.0.44, 1.1.414, 1.1.463, 1.1.463-r3.5.3-mkl, 1.1.463-r3.6.0-mkl

rstudioserver_epigenetics

1.0, 1.0-20171101

rsync

3.1.3

S

salome

9.2.0

samclip

0.2

samtools

0.1.18, 1.3.1, 1.6, 1.7, 1.7-gcc5, 1.9, 1.9-gcc5

sas

9.4

sbt

0.13.15, 1.2.1

scalapack

2.0.2

scipion

2.0, devel, devel-20170327, v1.0.1_2016-06-30, v1.1, v1.1.1, v1.2, v1.2.1, v1.2.1_2018-10-01

scrappie

1.4.1

sdm_1d_calculate restricted

2.0.2(default)

sdm_1d_plot restricted

0.0.4(default)

sdm_2d_calculate restricted

2.0.2(default)

sdm_2d_plot restricted

0.0.4(default)

seqgen

1.3.4

seqtk

1.3

shapeit

v2_r837

shovill

1.0.4

simnibs

2.0.1g

simple

2.1, 2.5

singlem

0.12.1

singularity

2.3.1, 2.4.2, 2.4.5, 2.5.2(default), 3.0, 3.0.1, 3.0.2, 3.1.0, 3.2.0, 3.2.1, d3d0f3fdc4390c7e14a6065543fc85dd69ba42b7

ska

1.0-e1968f0

skesa

2.2.1, 2.3

skewer

20170212

slamdunk

latest

slim

3.2

slurm

17.11.4

smux

0.0.1

snappy

master, master-gcc4

snippy

4.3.8

snp-dists

0.6.3

snpeff

4.3t

snpm

13

soapdenovo2

2.04-r241

sourcetracker

2.0.1

spades

3.12.0

sparseassembler

1.0

sparsehash

2.0.3

spider

21.11

spm12

matlab2015b.r6685, matlab2018a.r6685, matlab2018a.r7487

spm8

matlab2015b.r6685, matlab2017a.r6685

squashfs-tools

4.3-0.21

squashfuse

0.1.103

sra-tools

2.7.0, 2.9.2, 2.9.4

srst2

0.2.0, 0.2.0-2019

stacks

2.4

star

2.5.2b

stata restricted

14

stisuite

3.0

strelka

2.8.4

stringtie

1.3.5, 1.3.6

structure

2.3.4

subread

1.5.1

subversion

1.9.5

surfice

7_feb_2017

svd

1.4

swig

3.0.12

synopsys

3.1(default)

T

tannertools

2016.1, 2016.2

tapsim

v1.0b_r766

tbb

20180312oss

tempest

1.5

tensorflow

1.0.0-python2.7.12-gcc5, 1.10.0-pytorch, 1.10.0-pytorch-all, 1.10.0-pytorch-keras, 1.12.0-python2.7.12-gcc5, 1.12.0-python3.6-gcc5, 1.3.0-python2.7.12-gcc5, 1.4.0-python2.7.12-gcc5, 1.4.0-python3.6-gcc5

terastitcher

20171106

texlive

2017

tiff

4.0.8

tigervnc

1.8.0

tmap

3.0.1

toothmaker

0.64

topaz

1.0

tophat

2.1.1

tracer

1.6

trackvis

0.6.1

trim_galore

0.4.5, 0.5.0

trimmomatic

0.38

turbovnc

2.0.2(default), 2.1.0

tvips-tools

0.0.3

U

ucsc-genome-tools

201806

umap

0.3.8

umi-tools

0.5.5-python2, 0.5.5-python3

unblur

1.0.2

underworld

2.3.0

unicycler

0.4.7

unimelb-mf-clients

0.2.7

unrar

5.0

V

valgrind

3.13

varscan

2.3.9

vasp restricted

5.4.4

vcftools

0.1.15

vdjtools

1.2.1

vegas2

v02

velvet

1.2.10, 1.2.10-modified

vep

90(default), 94

vigra

1.9.0

vim

8.0.0596

virtualgl

2.5.0(default), 2.5.2

visit

2.12.3

vmd

1.9.3

volview

3.4

voro++

0.4.6

vt

0.57

vtk

5.10.1, 5.10.1-gcc4, 7.0.0, 7.0.0-gcc5

W

wasp

0.3.0

wfu_pickatlas

3.0.5b

workspace

4.0.2

wxgtk

3.0.2

wxwidgets

3.0.3

X

xds

20170302, monash(default), mxbeamteam

xjview

9.0, 9.6

xnat-desktop

0.96

xnat-utils

0.2.1, 0.2.5, 0.2.6, 0.4.5, 0.4.6, 0.4.9

xvfb

1.19.3

Y

yade

1.20.0-cpu, 1.20.0-gpu, yade-daily-may-2019

yasm

1.2.0-4

Z

zetastitcher

0.3.3

zlib

1.2.11

zoem

11-166

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