BEAR Applications

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There are open source and commercial applications installed for BEAR (including CaStLeS) users.

In the case of commercial applications, the number of licences purchased for use on BEAR platforms is constrained by the available budget and means we cannot guarantee availability of any particular licence from the shared pool at any specific time.

If guaranteed availability is required, for example for a long-term or time-critical project, IT Services recommends that users purchase their own licences which can be added to the service and reserved for nominated users. Similarly, IT Services reserves the right to request users whose sustained and heavy use of an application is having a detrimental effect on the shared service, to purchase licences to restore the balance.

Note that in many cases these licences are available at a greatly reduced cost compared to that of an individual purchase due to the economies of scale that come with a single University-wide account with the suppliers. The Software Sales web site has information about purchasing some of the applications that we make available on BEAR; contact the IT Service Desk for applications that are not covered by Software Sales.

To request the installation of a new application or an update to an existing one open a request with the IT Service Desk. Go to Make a Request > Advanced Research Computing Service > BEAR Software Services > Request a new or updated application.


List Of Currently Installed Applications
Application Most Recent Version
Abaqus R2017
ABINIT 8.6.1
ABySS 2.1.0
ADMIXTURE 1.3.0
ALLMAPS 0.8.4
Amber 18
ANGSD 0.919
ANNOVAR v2016Feb01
ANSYS 19.2
ANTs 2.3.1
Aspera Connect 3.8.0
AutoDock and AutoGrid, MGL Tools AutoDock/AutoGrid v4.2.5.1
MGL Tools v1.5.6
BAM2FASTQ 1.1.0
BAYENV v2.0 fbf60cdf8e27
BayeScan v2.1
BayPass v2.1
BayeScEnv v1.1
bcftools 1.2
bcl2fastq2 2.20.0
BEDOPS 2.4.30
bedtools 2.25.0
bgen 1.0.2
Bioconductor 3.7
BioPerl 1.7.1
Bismark 0.16.3
Blast - see NCBI Blast
BLAT 3.5
Blender 2.79
bokeh 0.13.0
BOOST Libraries 1.63.0
Bowtie 2 2.2.6
BreakDancer 1.1.2
Burrows-Wheeler Aligner (BWA) 0.7.17
BUSCO 1.0
Caffe 1.0
CASAVA 1.8.2
CASTEP 16.1
CcpNmr 2.4.2
CDO v1.7.2
CellRanger 2.1.1
cgatools 1.8.0.1
chiron 0.4.2
CIRCexplorer2 2.3.3
CIRCOS 0.69.2
Clustal Omega 1.1.0
ClustalW 2.1
CNVnator 0.3.3
CNV seq unversioned
cnvHiTSeq 0.1.2
COBALT 2.0.1
Comsol 5.0
cowplot 0.8.0
CP2K 5.1
CUDA Toolkit 9.2.88
cuDNN 7.1
Cufflinks 2.2.1
CULA toolkit Dense R17, Sparse S5
cutadapt 1.16
Cytoscape v3.2.0
DDSCAT v7.2.2
DEFORM v11.1.1
Delly2 v0.7.2
Diamond v0.8.28
discoSnp++ v2.2.4
DL_POLY Classic 1.9
DL_POLY 4 4.08
Eagle 2.3.2
EGADownloadClient 2.2.2
EIGENSOFT 6.1.4
ESS (Emacs Speaks Statistics) 12.09-2
eXpress 1.5.1
FastQC 0.11.5
FFTW 2 2.1.5
FFTW 3 3.3.7
FLASH 1.2.8
FlashPCA 2.0
Flow3D v11.0
FOSS (toolchain) 2018a
FreeBayes 49413aa
FreeSurfer v5.3.0
GAP 4.7.4
Gaussian G09 rev D.01
gcta 1.26.0
GenABEL 1.8-0
GeneTorrent 3.8.7
GENFIRE 1.1.11
Genome Analysis Toolkit 3.6
Genome MuSiC 0.4
Genome STRiP 2.00.1636
GffCompare 0.10.2
GGIR 1.4
Ghostscript 9.06.0
git 2.14.1
GMAP 2014-12-21
GNU Compiler Collection (gcc) 6.1.0
GMT 5.4.4
gnuplot 5.0.6
GNU Scientific Library 1.15
GPAW v0.10.0
GprMax v2.0
GRACE 5.1.25
graphmap 0.5.2
GROMACS 2018.3
GTOOL 0.7.5
gsutil 4.34
GULP 4.5.3
GWAMA 2.2.2
gvcfgenotyper 2018.01.07
gvcftools 0.16
Hail 489b8f0
HDFView 2.14
HEEDS v2017-4-2
HETS 0.99
HiCUP 0.6.0
HISAT2 2.1.0
HOMER 4.10.3
HTSeq 0.9.1
Hydra 0.5.5
icy 1.9.3.2
IGV 2.3.80
ilastik 1.2.2rc4
ImageMagick 7.0.7-39
IMPUTE2 2.3.2
Intel Compilers (toolchain) 2017.01
IOMKL (toolchain) 2018a
iRF 2.0.0
Isaac Aligner 03.17.03.01
Isaac Caller 1.0.7
Java 1.8.0-92
JAGS 3.4.0
jmol 14.28.3
julia 0.5.2
Kallisto 0.44.0
Kraken 0.10.5 beta
LADR (Library for Automated Deduction Research) v2009-11A
LAMMPS Stable_17Nov2016
LAPACK 3.6.1
libsvm 3.21
LM Suite 7.11
LoFreq 2.1.2
MACE4 - See LADR
MACS1 1.4.2
MACS2 2.1.1-20160309
MAKER 2.31.10
Manta 1.1.1
MaSuRCA 3.2.2
MATLAB R2018b
MCR (MATLAB Runtime) R2017b
MATS 4.0.2
MddNMR 2.5
MERLIN 1.1.2
METADISE 5.65
Metal 2011-03-25
MICRESS (not generally available) v6.302
minimap2 2.12
MOABS 1.2.7
MODA 1.2.0
MODELLER 9.19
MOPAC 2016 v16.299L
MPB 1.6.1
MUMmer 3.23
MUSCLE 3.8.31
MuTect 1.1.4
MutSig 1.4
NAG libraries various
NAMD 2.12
NanoPlot 1.17.2
nanopolish 0.10.1
nanoraw 0.5
NanoStat 1.1.2
NCAR Command Language 6.2.1
NCBI Blast 2.2.28
NCO 4.6.6
Ncview 2.1.2
Neper 3.0.0
NetCDF-C++ 4.2
Netgen 5.0.0
Nextflow 0.28.2
ngsplot 2.63
ngsutils 0.5.9
NLSEMagic 1D 020
nmrPipe 13092017
NWChem 6.8
Octave 3.8.2
oncodrivefml 2.0.3
OncoSNP 1.4
OncoSNP-Seq 2.01
OpenBUGS 3.2.2
OpenCV 3.4.1

OpenFOAM v5.0 20180108

v5.0 20180108

OpenFOAM v1806

v1806
OpenFOAM-Extend 4.0
OpenMPI 2.0.1
optimr 2016.8.16
Pandoc 2.3.1
ParaDiS 2.5.1
ParaView 5.4.1
PEAR 0.9.10
PennCNV 1.0.4
Perl 5.26.1
PGI Compiler Suite 17.7
PhyloSift 1.0.1
picard 2.10.5
pizzly 0.37.3
Platypus 0.8.1
PLINK 2.0a_20180930
Porechop 0.2.3
poretools 0.6.0
Portland Group compilers and tools 2013 v13.8
potfit 0.6.0
PRESTO 2.1
PrinSeq Lite 0.20.4
ProbABEL 0.5.0
prokka 1.12
ProtTest 3.2
Prover9 - see LADR
PyCharm 2017.2.1
PyMOL viewer 1.0.5.1

Python2

Extra Python Libraries are available on BlueBEAR, BEARCloud and CaStLeS VMs.

2.7.14

Python3

Extra Python Libraries are available on BlueBEAR, BEARCloud and CaStLeS VMs.

3.6.3
QCTOOL 2.0-rc8
QGIS 3.4.1
QIIME2 2018.4
QualiMap 2.1
QUICKTEST 1.1
QSTEM 2.30
Quantum Espresso 5.0.2

R

Extra R Libraries are available on BlueBEAR, BEARCloud and CaStLeS VMs.

3.5.0
readr 1.1.1
RepeatMasker 4.0.7
RepeatModeler 1.0.11
rgeos 0.3-23
Roary 3.12.0
ROOT 6.12.04
Rosetta 3.8
RSICNV unversioned
rstudio 1.1.453
SageMath 5.11
Sambamba 0.6.6
samblaster  0.1.24
SAMtools 1.8
Scilab 5.4.1
segemehl 0.2.0
Seismic_Unix 3c7a24e
SHAPEIT 2.r900
SHRiMP 2.2.3
SICER V1.1
SIESTA 3.1
sigproc 668de78
Singularity unversioned
SNP2HLA 1.0.3
snpEff 4.2
SNPhylo 20160204
snptest 2.5.2
SPAdes 3.10.1
Spark 2.2.0
SpeedSeq 0.1.2
SRA toolkit 2.4.5
STAR 2.6.0c
STAR-Fusion 1.4.0
StarCCM+ (not generally available) 12.04.010
Stata 15.0
Strelka 2.8.2
StringTie 1.3.3
Subread 1.5.3
Subversion 1.9.7
SUNDIALS 2.6.2
SUPPA 2.3
Sysweld/Sysworld v2014
Tempo 0e5ec0
Thermocalc (not generally available) v2017b
tmux 2.3
tombo 1.4
TopHat 2.1.1
Torch scientific computing framework 2.1.0
Trim Galore! 0.4.2
Trimmomatic v0.32
Trinity RNAseq 2.4.0
Turbomole 6.3
TwoSampleMR 0.4.8
Variant Effect Predictor 92
variant tools 2.6.1
VarScan 2.4.1
VASP 5.3.5
VASP Gamma Point 5.3.5
vcf2maf 1.6.16
VCFlib unversioned
VCFtools 0.1.15
VEP 94.5
VESTA 3.4.3
VineCopula f489e83
VMD 1.9.1
Weather Research and Forecasting (WRF) model 3.9.1
WGCNA 1.49
WGS 8.3rc2

Last modified: 22 July 2019