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Applications & Software

Installed Software and Applications

All software is installed centrally by the IT department in the cluster via Modules. If you need to request that a piece of software is installed, please reach out and request the software by sending an email to the IT Helpdesk at helpdesk@wistar.org.

Containers

Software has grown in complexity over the years making it difficult at times to install and run the software. Containers address this problem by storing the software and all of its dependencies (including a minimal operating system) in a single, large image so that there is nothing to install and when it comes time to run the software everything "just works". This makes the software both shareable and portable while the output becomes reproducible.

Containers can be utilized in the HPC Cluster with Apptainer (similar to docker). Please see the Apptainer page for more information.

Installing your own Software

You cannot install software in the Applications directory. If you need to request that a piece of software is installed, please reach out and request the software by sending a email to the IT Helpdesk at helpdesk@wistar.org.

NOTE: Do NOT install software in your Home Directory - there is a 10GB limit on home directories on purpose so that data and applications are not store there.

If your lab has need for their own software installation location, please reach out to the IT department, and we will configure a location to install applications. Please do not use your lab share to install applications - these are being backed up nightly and installed software does not need to be backed up.

Installed Modules

To find the most updated list of installed modules - you can run the following commands on the cluster:

Short List

module avail      # Shows ALL
module avail xyz  # Shows modules that contain xyz

List with Module Description

module spider      # Shows ALL with brief description
module spider xyz  # Shows modules that contain xyz - more detailed info

Load Module

module load xyz

Python Modules

Package Version
aiohttp 3.8.1
aiosignal 1.2.0
alabaster 0.7.12
anaconda-client 1.9.0
anaconda-navigator 2.1.4
anaconda-project 0.10.2
anyio 3.5.0
appdirs 1.4.4
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
arrow 1.2.2
astroid 2.6.6
astropy 5.0.4
asttokens 2.0.5
async-timeout 4.0.1
atomicwrites 1.4.0
attrs 21.4.0
Automat 20.2.0
autopep8 1.6.0
Babel 2.9.1
backcall 0.2.0
backports.functools-lru-cache 1.6.4
backports.tempfile 1
backports.weakref 1.0.post1
bcrypt 3.2.0
beautifulsoup4 4.11.1
binaryornot 0.4.4
bitarray 2.4.1
bkcharts 0.2
black 19.10b0
bleach 4.1.0
bokeh 2.4.2
boto3 1.21.32
botocore 1.24.32
Bottleneck 1.3.4
brotlipy 0.7.0
cachetools 4.2.2
certifi 2021.10.8
cffi 1.15.0
chardet 4.0.0
charset-normalizer 2.0.4
click 8.0.4
cloudpickle 2.0.0
clyent 1.2.2
colorama 0.4.4
colorcet 2.0.6
conda 4.12.0
conda-build 3.21.8
conda-content-trust 0+unknown
conda-pack 0.6.0
conda-package-handling 1.8.1
conda-repo-cli 1.0.4
conda-token 0.3.0
conda-verify 3.4.2
constantly 15.1.0
cookiecutter 1.7.3
cryptography 3.4.8
cssselect 1.1.0
cycler 0.11.0
Cython 0.29.28
cytoolz 0.11.0
daal4py 2021.5.0
dask 2022.2.1
datashader 0.13.0
datashape 0.5.4
debugpy 1.5.1
decorator 5.1.1
defusedxml 0.7.1
diff-match-patch 20200713
distributed 2022.2.1
docutils 0.17.1
entrypoints 0.4
et-xmlfile 1.1.0
executing 0.8.3
fastjsonschema 2.15.1
filelock 3.6.0
flake8 3.9.2
Flask 1.1.2
fonttools 4.25.0
frozenlist 1.2.0
fsspec 2022.2.0
future 0.18.2
gensim 4.1.2
glob2 0.7
gmpy2 2.1.2
google-api-core 1.25.1
google-auth 1.33.0
google-cloud-core 1.7.1
google-cloud-storage 1.31.0
google-crc32c 1.1.2
google-resumable-media 1.3.1
googleapis-common-protos 1.53.0
greenlet 1.1.1
grpcio 1.42.0
h5py 3.6.0
HeapDict 1.0.1
holoviews 1.14.8
hvplot 0.7.3
hyperlink 21.0.0
idna 3.3
imagecodecs 2021.8.26
imageio 2.9.0
imagesize 1.3.0
importlib-metadata 4.11.3
incremental 21.3.0
inflection 0.5.1
iniconfig 1.1.1
intake 0.6.5
intervaltree 3.1.0
ipykernel 6.9.1
ipython 8.2.0
ipython-genutils 0.2.0
ipywidgets 7.6.5
isort 5.9.3
itemadapter 0.3.0
itemloaders 1.0.4
itsdangerous 2.0.1
jdcal 1.4.1
jedi 0.18.1
jeepney 0.7.1
Jinja2 2.11.3
jinja2-time 0.2.0
jmespath 0.10.0
joblib 1.1.0
json5 0.9.6
jsonschema 4.4.0
jupyter 1.0.0
jupyter-client 6.1.12
jupyter-console 6.4.0
jupyter-core 4.9.2
jupyter-server 1.13.5
jupyterlab 3.3.2
jupyterlab-pygments 0.1.2
jupyterlab-server 2.10.3
jupyterlab-widgets 1.0.0
keyring 23.4.0
kiwisolver 1.3.2
lazy-object-proxy 1.6.0
libarchive-c 2.9
llvmlite 0.38.0
locket 0.2.1
lxml 4.8.0
Markdown 3.3.4
MarkupSafe 2.0.1
matplotlib 3.5.1
matplotlib-inline 0.1.2
mccabe 0.6.1
mistune 0.8.4
mkl-fft 1.3.1
mkl-random 1.2.2
mkl-service 2.4.0
mock 4.0.3
mpmath 1.2.1
msgpack 1.0.2
multidict 5.2.0
multipledispatch 0.6.0
munkres 1.1.4
mypy-extensions 0.4.3
navigator-updater 0.2.1
nbclassic 0.3.5
nbclient 0.5.13
nbconvert 6.4.4
nbformat 5.3.0
nest-asyncio 1.5.5
networkx 2.7.1
nltk 3.7
nose 1.3.7
notebook 6.4.8
numba 0.55.1
numexpr 2.8.1
numpy 1.21.5
numpydoc 1.2
olefile 0.46
openpyxl 3.0.9
packaging 21.3
pandas 1.4.2
pandocfilters 1.5.0
panel 0.13.0
param 1.12.0
parsel 1.6.0
parso 0.8.3
partd 1.2.0
pathspec 0.7.0
patsy 0.5.2
pep8 1.7.1
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.0.1
pip 21.2.4
pkginfo 1.8.2
plotly 5.6.0
pluggy 1.0.0
poyo 0.5.0
prometheus-client 0.13.1
prompt-toolkit 3.0.20
Protego 0.1.16
protobuf 3.19.1
psutil 5.8.0
ptyprocess 0.7.0
pure-eval 0.2.2
py 1.11.0
pyasn1 0.4.8
pyasn1-modules 0.2.8
pycodestyle 2.7.0
pycosat 0.6.3
pycparser 2.21
pyct 0.4.6
pycurl 7.44.1
PyDispatcher 2.0.5
pydocstyle 6.1.1
pyerfa 2.0.0
pyflakes 2.3.1
Pygments 2.11.2
PyHamcrest 2.0.2
PyJWT 2.1.0
pylint 2.9.6
pyls-spyder 0.4.0
pyodbc 4.0.32
pyOpenSSL 21.0.0
pyparsing 3.0.4
pyrsistent 0.18.0
PySocks 1.7.1
pytest 7.1.1
python-dateutil 2.8.2
python-lsp-black 1.0.0
python-lsp-jsonrpc 1.0.0
python-lsp-server 1.2.4
python-slugify 5.0.2
python-snappy 0.6.0
pytz 2021.3
pyviz-comms 2.0.2
PyWavelets 1.3.0
pyxdg 0.27
PyYAML 6
pyzmq 22.3.0
QDarkStyle 3.0.2
qstylizer 0.1.10
QtAwesome 1.0.3
qtconsole 5.3.0
QtPy 2.0.1
queuelib 1.5.0
regex 2022.3.15
requests 2.27.1
requests-file 1.5.1
rope 0.22.0
rsa 4.7.2
Rtree 0.9.7
ruamel-yaml-conda 0.15.100
s3transfer 0.5.0
scikit-image 0.19.2
scikit-learn 1.0.2
scikit-learn-intelex 2021.20220215.212715
scipy 1.7.3
Scrapy 2.6.1
seaborn 0.11.2
SecretStorage 3.3.1
Send2Trash 1.8.0
service-identity 18.1.0
setuptools 61.2.0
sip 4.19.13
six 1.16.0
smart-open 5.1.0
sniffio 1.2.0
snowballstemmer 2.2.0
sortedcollections 2.1.0
sortedcontainers 2.4.0
soupsieve 2.3.1
Sphinx 4.4.0
sphinxcontrib-applehelp 1.0.2
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 2.0.0
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.5
spyder 5.1.5
spyder-kernels 2.1.3
SQLAlchemy 1.4.32
stack-data 0.2.0
statsmodels 0.13.2
sympy 1.10.1
tables 3.6.1
tabulate 0.8.9
TBB 0.2
tblib 1.7.0
tenacity 8.0.1
terminado 0.13.1
testpath 0.5.0
text-unidecode 1.3
textdistance 4.2.1
threadpoolctl 2.2.0
three-merge 0.1.1
tifffile 2021.7.2
tinycss 0.4
tldextract 3.2.0
toml 0.10.2
tomli 1.2.2
toolz 0.11.2
tornado 6.1
tqdm 4.64.0
traitlets 5.1.1
Twisted 22.2.0
typed-ast 1.4.3
typing_extensions 4.1.1
ujson 5.1.0
Unidecode 1.2.0
urllib3 1.26.9
w3lib 1.21.0
watchdog 2.1.6
wcwidth 0.2.5
webencodings 0.5.1
websocket-client 0.58.0
Werkzeug 2.0.3
wheel 0.37.1
widgetsnbextension 3.5.2
wrapt 1.12.1
wurlitzer 3.0.2
xarray 0.20.1
xlrd 2.0.1
XlsxWriter 3.0.3
yapf 0.31.0
yarl 1.6.3
zict 2.0.0
zipp 3.7.0
zope.interface 5.4.0

R Packages

Here is the list of installed R Packages:

Package Version
abc 2.2.1
abc.data 1.0
abe 3.0.1
abind 1.4-5
acepack 1.4.1
adabag 4.2
ade4 1.7-19
ADGofTest 0.3
admisc 0.29
aggregation 1.0.1
AICcmodavg 2.3-1
akima 0.6-3.4
alabama 2022.4-1
AlgDesign 1.2.1
alluvial 0.1-2
animation 2.7
aod 1.3.2
apcluster 1.4.10
ape 5.6-2
argparse 2.1.5
arm 1.12-2
askpass 1.1
asnipe 1.1.16
assertive 0.3-6
assertive.base 0.0-9
assertive.code 0.0-3
assertive.data 0.0-3
assertive.data.uk 0.0-2
assertive.data.us 0.0-2
assertive.datetimes 0.0-3
assertive.files 0.0-2
assertive.matrices 0.0-2
assertive.models 0.0-2
assertive.numbers 0.0-2
assertive.properties 0.0-5
assertive.reflection 0.0-5
assertive.sets 0.0-3
assertive.strings 0.0-3
assertive.types 0.0-3
assertthat 0.2.1
AUC 0.3.2
audio 0.1-10
aws 2.5-1
awsMethods 1.1-1
backports 1.4.1
bacr 1.0.1
bartMachine 1.2.6
bartMachineJARs 1.1
base64 2.0
base64enc 0.1-3
BatchJobs 1.9
batchmeans 1.0-4
BayesianTools 0.1.7
BayesLogit 2.1
bayesm 3.1-4
BayesPen 1.0
bayesplot 1.9.0
BB 2019.10-1
BBmisc 1.12
bbmle 1.0.25
BCEE 1.3.0
BDgraph 2.67
bdsmatrix 1.3-6
beanplot 1.3.1
beeswarm 0.4.0
betareg 3.1-4
BH 1.78.0-0
BiasedUrn 1.07
bibtex 0.4.2.3
BIGL 1.6.6
bigmemory 4.6.1
bigmemory.sri 0.1.3
bindr 0.1.1
bindrcpp 0.2.2
bio3d 2.4-3
biom 0.3.12
biomod2 3.5.1
bit 4.0.4
bit64 4.0.5
bitops 1.0-7
blavaan 0.4-3
blob 1.2.3
BMA 3.18.17
bmp 0.3
bnlearn 4.7.1
bold 1.2.0
bootstrap 2019.6
Boruta 7.0.0
brew 1.0-7
brglm 0.7.2
bridgedist 0.1.1
bridgesampling 1.1-2
brio 1.1.3
brms 2.17.0
Brobdingnag 1.2-7
broom 0.8.0
broom.helpers 1.7.0
broom.mixed 0.2.9.4
bslib 0.3.1
bst 0.3-23
cachem 1.0.6
Cairo 1.5-15
calibrate 1.7.7
callr 3.7.0
car 3.1-0
carData 3.0-5
caret 6.0-92
catlearn 0.9.1
caTools 1.18.2
CBPS 0.23
celestial 1.4.6
cellranger 1.1.0
cgdsr 1.3.0
cghFLasso 0.2-1
checkmate 2.1.0
chemometrics 1.4.2
chkptstanr 0.1.1
chron 2.3-57
circlize 0.4.15
circular 0.4-95
classInt 0.4-7
cli 3.3.0
clipr 0.8.0
clisymbols 1.2.0
clue 0.3-61
clusterGeneration 1.3.7
clusterRepro 0.9
clustree 0.4.4
clValid 0.7
cmprsk 2.2-11
cNORM 3.0.2
cobalt 4.3.2
cobs 1.3-5
coda 0.19-4
coin 1.4-2
collapse 1.8.6
colorspace 2.0-3
colourpicker 1.1.1
combinat 0.0-8
ComICS 1.0.4
commonmark 1.8.0
compositions 2.0-4
CompQuadForm 1.4.3
conditionz 0.1.0
conquer 1.3.0
contfrac 1.1-12
copCAR 2.0-4
copula 1.1-0
corpcor 1.6.10
corrplot 0.92
covr 3.5.1
CovSel 1.2.1
covsim 1.0.0
cowplot 1.1.1
coxed 0.3.3
cpp11 0.4.2
crayon 1.5.1
credentials 1.3.2
crosstalk 1.2.0
crul 1.2.0
cSEM 0.4.0
csSAM 1.2.4
ctmle 0.1.2
cubature 2.0.4.4
cubelyr 1.0.1
curl 4.3.2
cvAUC 1.1.4
CVST 0.2-3
d3Network 0.5.2.1
dagitty 0.3-1
data.table 1.14.2
data.tree 1.0.0
DataCombine 0.2.21
date 1.2-39
dbarts 0.9-22
DBI 1.1.3
dbplyr 2.2.0
dcurver 0.9.2
ddalpha 1.3.13
deal 1.2-39
debugme 1.1.0
deldir 1.0-6
dendextend 1.15.2
DEoptim 2.2-6
DEoptimR 1.0-11
Deriv 4.1.3
desc 1.4.1
DescTools 0.99.45
deSolve 1.32
devtools 2.4.3
dfidx 0.0-4
DHARMa 0.4.5
dHSIC 2.1
diagram 1.6.5
DiagrammeR 1.0.9
DiceKriging 1.6.0
dichromat 2.0-0.1
diffobj 0.3.5
digest 0.6.29
dimRed 0.2.5
diptest 0.76-0
DiscriMiner 0.1-29
dismo 1.3-5
distillery 1.2-1
distr 2.8.0
distrEx 2.8.0
distributional 0.3.0
DistributionUtils 0.6-0
diveRsity 1.9.90
DMCfun 2.0.2
docstring 1.0.0
doMC 1.3.8
doParallel 1.0.17
doRNG 1.8.2
doSNOW 1.0.20
dotCall64 1.0-1
downloader 0.4
dplyr 1.0.9
dr 3.0.10
drgee 1.1.10
DRR 0.0.4
drugCombo 1.2.1
DT 0.23
dtangle 2.0.9
dtplyr 1.2.1
DTRreg 1.7
dtw 1.22-3
dummies 1.5.6
dygraphs 1.1.1.6
dynamicTreeCut 1.63-1
e1071 1.7-11
earth 5.3.1
EasyABC 1.5
elementR 1.3.7
ellipse 0.4.3
ellipsis 0.3.2
elliptic 1.4-0
emdbook 1.3.12
emulator 1.2-21
energy 1.7-10
ENMeval 2.0.3
entropy 1.3.1
EnvStats 2.7.0
ergm 4.2.2
ergm.count 4.1.1
evaluate 0.15
EValue 4.1.3
evd 2.3-6
Exact 3.1
expm 0.999-6
ExPosition 2.8.23
expsmooth 2.3
extrafont 0.18
extrafontdb 1.0
extRemes 2.1-2
FactoMineR 2.4
FactorCopula 0.8
fail 1.3
fansi 1.0.3
farver 2.1.0
fastcluster 1.2.3
fasterize 1.0.3
fastICA 1.2-3
fastmap 1.1.0
fastmatch 1.1-3
fdrtool 1.2.17
feather 0.3.5
ff 4.0.7
ffbase 0.13.3
fftw 1.0-7
fftwtools 0.9-11
fields 13.3
filehash 2.4-3
finalfit 1.0.4
findpython 1.0.7
fishMod 0.29
fitdistrplus 1.1-8
flashClust 1.01-2
flexclust 1.4-1
flexmix 2.3-18
fma 2.4
FME 1.3.6.2
fmri 1.9.6
FNN 1.1.3.1
fontawesome 0.2.2
forcats 0.5.1
foreach 1.5.2
forecast 8.16
formatR 1.12
Formula 1.2-4
formula.tools 1.7.1
fossil 0.4.0
fpc 2.2-9
fpp 0.5
fracdiff 1.5-1
fs 1.5.2
furrr 0.3.0
futile.logger 1.4.3
futile.options 1.0.1
future 1.26.1
future.apply 1.9.0
gam 1.20.1
gamlss 5.4-3
gamlss.data 6.0-2
gamlss.dist 6.0-3
gamlss.tr 5.1-7
gamm4 0.2-6
gap 1.2.3-6
gap.datasets 0.0.5
gapfill 0.9.6-1
gargle 1.2.0
gaussquad 1.0-3
gbm 2.1.8
gbRd 0.4-11
gclus 1.3.2
gdalUtils 2.0.3.2
gdata 2.18.0.1
gdistance 1.3-6
gee 4.13-23
geepack 1.3.4
geex 1.0.12
geiger 2.0.10
GeneNet 1.2.16
generics 0.1.2
genoPlotR 0.8.11
GenSA 1.1.7
geojsonsf 2.0.3
geometries 0.2.0
geometry 0.4.6
gert 1.6.0
getopt 1.20.3
GetoptLong 1.0.5
GGally 2.1.2
ggbeeswarm 0.6.0
ggdag 0.2.4
ggExtra 0.10.0
ggfan 0.1.3
ggforce 0.3.3
ggnetwork 0.5.10
ggplot2 3.3.6
ggpubr 0.4.0
ggraph 2.0.5
ggrepel 0.9.1
ggridges 0.5.3
ggsci 2.9
ggsignif 0.6.3
ggvis 0.4.7
gh 1.3.0
GillespieSSA 0.6.2
git2r 0.30.1
gitcreds 0.1.1
GJRM 0.2-6
glasso 1.11
gld 2.6.4
gllvm 1.3.1
glmmML 1.1.3
glmmTMB 1.1.3
glmnet 4.1-4
GlobalOptions 0.1.2
globals 0.15.0
glue 1.6.2
gmm 1.6-6
gmodels 2.18.1.1
gmp 0.6-5
gnumeric 0.7-8
goftest 1.2-3
gomms 1.0
googledrive 2.0.0
googlesheets4 1.0.0
gower 1.0.0
GPArotation 2022.4-1
gplots 3.1.3
graphlayouts 0.8.0
grf 2.1.0
gridBase 0.4-7
gridExtra 2.3
grImport2 0.2-0
grpreg 3.4.0
GSA 1.03.2
gsalib 2.1
gsl 2.1-7.1
gsw 1.0-6
gt 0.6.0
gtable 0.3.0
gtools 3.9.2.2
gtsummary 1.6.1
GUTS 1.2.3
gWidgets2 1.0-9
gWidgets2tcltk 1.0-8
GxEScanR 2.0.2
h2o 3.36.1.2
hal9001 0.4.3
hardhat 1.1.0
harmony 0.1.0
hash 2.2.6.2
haven 2.5.0
hdf5r 1.3.5
hdm 0.3.1
heatmap3 1.1.9
here 1.0.1
hexbin 1.28.2
HiddenMarkov 1.8-13
highr 0.9
Hmisc 4.7-0
hms 1.1.1
Hmsc 3.0-11
htmlTable 2.4.0
htmltools 0.5.2
htmlwidgets 1.5.4
httpcode 0.3.0
httpuv 1.6.5
httr 1.4.3
huge 1.3.5
hunspell 3.0.1
hwriter 1.3.2.1
HWxtest 1.1.9
hypergeo 1.2-13
ica 1.0-2
IDPmisc 1.1.20
idr 1.3
ids 1.0.1
ie2misc 0.8.8
igraph 1.3.2
image.binarization 0.1.2
imager 0.42.13
imagerExtra 1.3.2
ineq 0.2-13
influenceR 0.1.0.1
infotheo 1.2.0.1
ini 0.3.1
inline 0.3.19
intergraph 2.0-2
interpretR 0.2.4
intrinsicDimension 1.2.0
inum 1.0-4
ipred 0.9-13
irace 3.4.1
irlba 2.3.5
ismev 1.42
Iso 0.0-18.1
isoband 0.2.5
ISOcodes 2022.01.10
iterators 1.0.14
itertools 0.1-3
JADE 2.0-3
janeaustenr 0.1.5
JBTools 0.7.2.9
jiebaR 0.11
jiebaRD 0.1
jomo 2.7-3
jpeg 0.1-9
jquerylib 0.1.4
jsonify 1.2.1
jsonlite 1.8.0
jstable 1.0.7
kde1d 1.0.4
kedd 1.0.3
kernlab 0.9-31
klaR 1.7-0
knitr 1.39
KODAMA 1.9
kohonen 3.0.11
ks 1.13.5
labdsv 2.0-1
labeling 0.4.2
labelled 2.9.1
laeken 0.5.2
lambda.r 1.2.4
LaplacesDemon 16.1.6
lars 1.3
lassosum 0.4.5
later 1.3.0
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