Installed Applications: 2020a and Ubuntu20.04-haswell

Applications available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). All 2020a or Ubuntu20.04-haswell applications. In any one job, or session, you should use applications from only one BEAR Apps Version.

Application Version
ald 1.2-foss-2020a-R-4.0.0
angsd 0.933-GCC-9.3.0
ant 1.10.8-Java-11
astropy 4.0-foss-2020a-Python-3.8.2
ATK 2.36.0-GCCcore-9.3.0
at-spi2-atk 2.34.2-GCCcore-9.3.0
at-spi2-core 2.36.0-GCCcore-9.3.0
Autoconf 2.69-GCCcore-9.3.0
autograd 1.3-foss-2020a-Python-3.8.2
Automake 1.16.1-GCCcore-9.3.0
Autotools 20180311-GCCcore-9.3.0
BamTools 2.5.1-GCC-9.3.0
Bazel 3.6.0-GCCcore-9.3.0
BCFtools 1.10.2-GCC-9.3.0
bcl2fastq2 2.20.0-GCC-9.3.0
beagle-lib 3.1.2-GCC-9.3.0
BEAR-Python-DataScience 2020a-foss-2020a-Python-3.8.2
BEAR-R-bio 2020a-foss-2020a-R-4.0.0
BeautifulSoup 4.9.1-GCCcore-9.3.0-Python-3.8.2
BEDTools 2.29.2-GCC-9.3.0
betapart 1.5.2-foss-2020a-R-4.0.0
bigsnpr 1.8.1-foss-2020a-R-4.0.0
bigsnpr 1.6.1-foss-2020a-R-4.0.0
binutils 2.34-GCCcore-9.3.0
binutils 2.34
BioPerl 1.7.7-GCCcore-9.3.0
Biopython 1.78-foss-2020a-Python-3.8.2
BioServices 1.7.9-foss-2020a-Python-3.8.2
Bison 3.5.3-GCCcore-9.3.0
Bison 3.5.3
Bison 3.3.2
BLAST+ 2.10.1-gompi-2020a
bokeh 2.0.2-foss-2020a-Python-3.8.2
Boost 1.72.0-gompi-2020a
BWA 0.7.17-foss-2020a
bzip2 1.0.8-GCCcore-9.3.0
cairo 1.16.0-GCCcore-9.3.0
Canvas 1.40.0.1613
Cardinal 2.6.0-foss-2020a-R-4.0.0
CD-HIT 4.8.1-GCC-9.3.0
CellChat 20210814-foss-2020a-R-4.0.0
CellRanger 5.0.1
CellRanger-ARC 1.0.1
CellRanger-ATAC 2.0.0
CellRanger-ATAC 1.2.0
ChAMP 2.18.3-foss-2020a-R-4.0.0
CMake 3.16.4-GCCcore-9.3.0
CNVkit 0.9.8-foss-2020a-Python-3.8.2-R-4.0.0
cURL 7.69.1-GCCcore-9.3.0
Cython 0.27.3-GCCcore-9.3.0-Python-2.7.18
dask 2.18.1-foss-2020a-Python-3.8.2
DB 18.1.32-GCCcore-9.3.0
DB_File 1.835-GCCcore-9.3.0
DBus 1.13.12-GCCcore-9.3.0
deepTools 3.5.0-foss-2020a-Python-3.8.2
DirichletMultinomial 1.32.0-foss-2020a-R-4.0.0
DivNet 31e04e2-foss-2020a-R-4.0.0
doFuture 0.10.0-foss-2020a-R-4.0.0
double-conversion 3.1.5-GCCcore-9.3.0
Doxygen 1.8.17-GCCcore-9.3.0
DROP 1.0.3-foss-2020a-Python-3.8.2-R-4.0.0
Eigen 3.3.7-GCCcore-9.3.0
EIGENSOFT 7.2.1-foss-2020a
EnhancedVolcano 1.6.0-foss-2020a-R-4.0.0
expat 2.2.9-GCCcore-9.3.0
faahKO 1.28.0-foss-2020a-R-4.0.0
factoextra 1.0.7-foss-2020a-R-4.0.0
fastStructure 1.0-foss-2020a-Python-2.7.18
FastTree 2.1.11-GCCcore-9.3.0
FFmpeg 4.2.2-GCCcore-9.3.0
FFTW 3.3.8-gompi-2020a
flatbuffers 1.12.0-GCCcore-9.3.0
flex 2.6.4-GCCcore-9.3.0
flex 2.6.4
fmi2 0.2.0-foss-2020a-R-4.0.0
fontconfig 2.13.92-GCCcore-9.3.0
foss 2020a
freetype 2.10.1-GCCcore-9.3.0
FriBidi 1.0.9-GCCcore-9.3.0
furrr 0.2.1-foss-2020a-R-4.0.0
gambin 2.4.4-foss-2020a-R-4.0.0
GATK 4.1.5.0-GCCcore-9.3.0-Java-11
gc 7.6.12-GCCcore-9.3.0
GCC 9.3.0
GCCcore 9.3.0
GDAL 3.0.4-foss-2020a-Python-3.8.2
Gdk-Pixbuf 2.40.0-GCCcore-9.3.0
gdm 1.4.2-foss-2020a-R-4.0.0
gensim 4.0.1-foss-2020a-Python-3.8.2
GeoMxNGSPipeline 2.2
GEOS 3.8.1-GCC-9.3.0-Python-3.8.2
geosphere 1.5-10-foss-2020a-R-4.0.0
gettext 0.20.1-GCCcore-9.3.0
gettext 0.20.1
GFOLD 1.1.4-GCC-9.3.0
ggvenn 0.1.8-foss-2020a-R-4.0.0
Ghostscript 9.52-GCCcore-9.3.0
giflib 5.2.1-GCCcore-9.3.0
git 2.23.0-GCCcore-9.3.0-nodocs
GitPython 3.1.9-GCCcore-9.3.0-Python-3.8.2
GLib 2.64.1-GCCcore-9.3.0
GLPK 4.65-GCCcore-9.3.0
GMP 6.2.0-GCCcore-9.3.0
gmpy2 2.1.0b5-GCC-9.3.0
Go 1.14.1
GObject-Introspection 1.64.0-GCCcore-9.3.0-Python-3.8.2
gompi 2020a
GPArotation 2014.11-1-foss-2020a-R-4.0.0
gperf 3.1-GCCcore-9.3.0
graphite2 1.3.14-GCCcore-9.3.0
Graphviz 2.44.1-foss-2020a
GSL 2.6-GCC-9.3.0
GTK+ 3.24.17-GCCcore-9.3.0
GTS 0.7.6-foss-2020a
Guile 2.2.4-GCCcore-9.3.0
gwpv 0.2.0-foss-2020a-Python-3.8.2
gzip 1.10-GCCcore-9.3.0
h5py 2.10.0-foss-2020a-Python-3.8.2
HarfBuzz 2.6.4-GCCcore-9.3.0
Harminv 1.4.1-foss-2020a
HDF5 1.10.6-gompi-2020a
help2man 1.47.4
help2man 1.47.12-GCCcore-9.3.0
HOMER 4.11-foss-2020a
HPL 2.3-foss-2020a
HTSlib 1.10.2-GCC-9.3.0
hwloc 2.2.0-GCCcore-9.3.0
ICU 66.1-GCCcore-9.3.0
IGV 2.8.0-Java-11
ImageMagick 7.0.10-1-GCCcore-9.3.0
intltool 0.51.0-GCCcore-9.3.0
IPython 7.13.0-foss-2020a-Python-3.8.2
iRF 3.0.0-foss-2020a-R-4.0.0
iterativeWGCNA 1.1.6-foss-2020a-Python-3.8.2-R-4.0.0
JAGS 4.3.0-foss-2020a
JasPer 2.0.14-GCCcore-9.3.0
Java 1.8.0_241
Java 1.8
Java 11.0.2
Java 11
JsonCpp 1.9.4-GCCcore-9.3.0
kinship2 1.8.5-foss-2020a-R-4.0.0
Kraken 1.1.1-GCCcore-9.3.0
LAME 3.100-GCCcore-9.3.0
leafcutter 0.2.9-foss-2020a-R-4.0.0-Python-2.7.18
libctl 4.5.0-GCCcore-9.3.0
libdrm 2.4.100-GCCcore-9.3.0
libepoxy 1.5.4-GCCcore-9.3.0
libevent 2.1.11-GCCcore-9.3.0
libffi 3.3-GCCcore-9.3.0
libgd 2.3.0-GCCcore-9.3.0
libGDSII 0.21-GCCcore-9.3.0
libgeotiff 1.5.1-GCCcore-9.3.0
libGLU 9.0.1-GCCcore-9.3.0
libglvnd 1.2.0-GCCcore-9.3.0
libidn 1.35-GCCcore-9.3.0
libjpeg-turbo 2.0.4-GCCcore-9.3.0
libpciaccess 0.16-GCCcore-9.3.0
libpng 1.6.37-GCCcore-9.3.0
libreadline 8.0-GCCcore-9.3.0
libsndfile 1.0.28-GCCcore-9.3.0
libsodium 1.0.18-GCCcore-9.3.0
LibTIFF 4.1.0-GCCcore-9.3.0
libtirpc 1.2.6-GCCcore-9.3.0
libtool 2.4.6-GCCcore-9.3.0
libunistring 0.9.10-GCCcore-9.3.0
libunwind 1.3.1-GCCcore-9.3.0
libxml2 2.9.10-GCCcore-9.3.0
libxslt 1.1.34-GCCcore-9.3.0
libyaml 0.2.2-GCCcore-9.3.0
LIGGGHTS 3.8.0-foss-2020a
LittleCMS 2.9-GCCcore-9.3.0
LLVM 9.0.1-GCCcore-9.3.0
LMDB 0.9.24-GCCcore-9.3.0
LoFreq 2.1.5-foss-2020a-Python-2.7.18
lxml 4.5.2-GCCcore-9.3.0
lz4 1.9.2-GCCcore-9.3.0
M3C 1.10.0-foss-2020a-R-4.0.0
M4 1.4.18-GCCcore-9.3.0
M4 1.4.18
MAFFT 7.453-GCC-9.3.0-with-extensions
MAJIQ 2.2-foss-2020a-54fd98d-Python-3.8.2
Mako 1.1.2-GCCcore-9.3.0
MariaDB-connector-c 3.1.7-GCCcore-9.3.0
mass2adduct 20210609-foss-2020a-R-4.0.0
MAST 1.14.0-foss-2020a-R-4.0.0
matplotlib 3.2.1-foss-2020a-Python-3.8.2
matplotlib 2.2.5-foss-2020a-Python-2.7.18
MCL 14.137-GCCcore-9.3.0
MCR R2019a
MCR R2013b
mddnmr 2.7-foss-2020a-Python-2.7.18
Meep 1.17.1-foss-2020a-Python-3.8.2
MERLIN 1.1.2-GCCcore-9.3.0
Mesa 20.0.2-GCCcore-9.3.0
Meson 0.53.2-GCCcore-9.3.0-Python-3.8.2
microbenchmark 1.4.9-foss-2020a-R-4.0.0
Miniconda3 4.9.2
mlxtend 0.17.3-foss-2020a-Python-3.8.2
MPB 1.11.1-foss-2020a-Python-3.8.2
MPC 1.1.0-GCC-9.3.0
MPFR 4.0.2-GCCcore-9.3.0
MrBayes 3.2.7a-foss-2020a
NASM 2.14.02-GCCcore-9.3.0
ncdf4 1.17-foss-2020a-R-4.0.0
ncurses 6.2-GCCcore-9.3.0
ncurses 6.1
netCDF 4.7.4-gompi-2020a
netCDF-Fortran 4.5.2-gompi-2020a
Net-core 2.1.28
networkx 2.4-foss-2020a-Python-3.8.2
Ninja 1.10.0-GCCcore-9.3.0
NLopt 2.6.1-GCCcore-9.3.0
NLopt 2.6.1-foss-2020a-Python-3.8.2
NMRPipe 20022021-foss-2020a
NSPR 4.25-GCCcore-9.3.0
NSS 3.51-GCCcore-9.3.0
nsync 1.24.0-GCCcore-9.3.0
numactl 2.0.13-GCCcore-9.3.0
numba 0.50.0-foss-2020a-Python-3.8.2
OncoSNP-Seq 2.01
OpenBLAS 0.3.9-GCC-9.3.0
OpenCV 4.4.0-foss-2020a-Python-3.8.2
OpenJPEG 2.4.0-GCCcore-9.3.0
OpenMPI 4.0.5-GCC-9.3.0
OpenMPI 4.0.3-GCC-9.3.0
OpenPGM 5.2.122-GCCcore-9.3.0
ottr 1.0.0-foss-2020a-R-4.0.0
pander 0.6.4-foss-2020a-R-4.0.0
Pandoc 2.10
Pango 1.44.7-GCCcore-9.3.0
parallel 20200522-GCCcore-9.3.0
ParaView 5.8.0-foss-2020a-Python-3.8.2-mpi-offscreen
PCAmixdata 3.1-foss-2020a-R-4.0.0
PCRE 8.44-GCCcore-9.3.0
PCRE2 10.34-GCCcore-9.3.0
pept 0.3.2-foss-2020a-Python-3.8.2
pept 0.2.4-foss-2020a-Python-3.8.2
Perl 5.30.2-GCCcore-9.3.0
PHATE 1.0.7-foss-2020a-Python-3.8.2
phateR 1.0.7-foss-2020a-R-4.0.0-Python-3.8.2
Pillow 7.0.0-GCCcore-9.3.0-Python-3.8.2
pixman 0.38.4-GCCcore-9.3.0
pkg-config 0.29.2-GCCcore-9.3.0
pkgconfig 1.5.1-GCCcore-9.3.0-Python-3.8.2
plotly.py 4.8.1-GCCcore-9.3.0
poppler 0.90.1-GCCcore-9.3.0
PRANK 170427-GCC-9.3.0
PReMiuM 3.2.3-foss-2020a-R-4.0.0
ProbABEL 0.5.0-GCCcore-9.3.0
profvis 0.3.7-foss-2020a-R-4.0.0
PROJ 7.0.0-GCCcore-9.3.0
protobuf 3.13.0-GCCcore-9.3.0
protobuf-python 3.13.0-foss-2020a-Python-3.8.2
PRROC 1.3.1-foss-2020a-R-4.0.0
PRSice 2.3.3-GCCcore-9.3.0
pybind11 2.4.3-GCCcore-9.3.0-Python-3.8.2
Pysam 0.16.0.1-GCC-9.3.0
Python 3.8.2-GCCcore-9.3.0
Python 2.7.18-GCCcore-9.3.0
python-bioformats 4.0.0-foss-2020a-Python-3.8.2
PyYAML 5.3-GCCcore-9.3.0
QIIME2 2021.2
qqman 0.1.8-foss-2020a-R-4.0.0
Qt5 5.14.1-GCCcore-9.3.0
qtl2 0.28-foss-2020a-R-4.0.0
R 4.0.0-foss-2020a
RAPID fcd9e9b-foss-2020a-R-4.0.0
R-bundle-Bioconductor 3.11-foss-2020a-R-4.0.0
RcisTarget 1.8.0-foss-2020a-R-4.0.0
RcppAnnoy 0.0.19-foss-2020a-R-4.0.0
re2c 1.3-GCCcore-9.3.0
regtools 0.5.2-foss-2020a
rethinking 2.13-foss-2020a-R-4.0.0
rgdal 1.5-16-foss-2020a-R-4.0.0
rjags 4-10-foss-2020a-R-4.0.0
Roary 3.13.0-foss-2020a
Rphenoannoy 20210906-foss-2020a-R-4.0.0
Rphenograph 20210906-foss-2020a-R-4.0.0
rpy2 3.3.6-foss-2020a-Python-3.8.2
rstudio 1.3.959-foss-2020a-Java-11-R-4.0.0
SAMtools 1.10-GCC-9.3.0
sars 1.2.3-foss-2020a-R-4.0.0
ScaLAPACK 2.1.0-gompi-2020a
scCATCH 2.1-foss-2020a-R-4.0.0
scikit-image 0.17.1-foss-2020a-Python-3.8.2
scikit-learn 0.23.2-foss-2020a-Python-3.8.2
SciPy-bundle 2020.03-foss-2020a-Python-3.8.2
SciPy-bundle 2020.03-foss-2020a-Python-2.7.18
Seaborn 0.11.0-foss-2020a-Python-3.8.2
segemehl 0.3.4-GCC-9.3.0
sequenza 3.0.0-foss-2020a-R-4.0.0
sequenza-utils 3.0.0-foss-2020a-Python-3.8.2-R-4.0.0
Seurat 4.0.0-foss-2020a-R-4.0.0
SeuratDisk 0.0.0.9018-foss-2020a-R-4.0.0
sf 0.9-5-foss-2020a-R-4.0.0-Python-3.8.2
slingshot 1.6.1-foss-2020a-R-4.0.0
snakemake 5.31.1-foss-2020a-Python-3.8.2
snappy 1.1.8-GCCcore-9.3.0
SpaceRanger 1.2.2-GCC-9.3.0
spdep 1.1-5-foss-2020a-R-4.0.0-Python-3.8.2
SQLite 3.31.1-GCCcore-9.3.0
structToolbox 1.0.1-foss-2020a-R-4.0.0
SWIG 4.0.1-GCCcore-9.3.0
sympy 1.6.2-foss-2020a-Python-3.8.2
Szip 2.1.1-GCCcore-9.3.0
Tcl 8.6.10-GCCcore-9.3.0
tcsh 6.22.02-GCCcore-9.3.0
texlive 20200406-GCCcore-9.3.0
tidymodels 0.1.0-foss-2020a-R-4.0.0
time 1.9-GCCcore-9.3.0
Tk 8.6.10-GCCcore-9.3.0
Tkinter 3.8.2-GCCcore-9.3.0
Tkinter 2.7.18-GCCcore-9.3.0
tqdm 4.47.0-GCCcore-9.3.0
UDUNITS 2.2.26-GCCcore-9.3.0
unrar 6.0.7-GCCcore-9.3.0
util-linux 2.35-GCCcore-9.3.0
VTK 8.2.0-foss-2020a-Python-3.8.2
WGCNA 1.70-3-foss-2020a-R-4.0.0
wget 1.20.3-GCCcore-9.3.0
WPS 3.9.1-foss-2020a-dmpar
WRF 3.9.1.1-foss-2020a-dmpar
X11 20200222-GCCcore-9.3.0
x264 20191217-GCCcore-9.3.0
x265 3.3-GCCcore-9.3.0
XML-LibXML 2.0205-GCCcore-9.3.0
xorg-macros 1.19.2-GCCcore-9.3.0
xterm 366-foss-2020a
XZ 5.2.5-GCCcore-9.3.0
Yasm 1.3.0-GCCcore-9.3.0
ZeroMQ 4.3.2-GCCcore-9.3.0
Zip 3.0-GCCcore-9.3.0
zlib 1.2.11-GCCcore-9.3.0
zlib 1.2.11
zstd 1.4.4-GCCcore-9.3.0