Installed Software

CRC uses the lmod environment modules system to provision software to our users (https://crc.pitt.edu/h2p#appenv).  To query whether a software is available, use

module spider <name_of_software>

Listed below are all the installed software as of 09/10/2020 on our system:

  abaqus
  abinit
  abinit-epg
  abyss
  adf
  admixmap
  advisor
  af4
  afni
  albacore
  amber
  ancestrymap
  annovar
  ansys
  ansysem
  ants
  arboreto
  aria2
  arpack
  aspeak
  atacseq_harvard
  augustus
  autodock_vina
  awscli
  bamqc
  bamtools
  bamutil
  basespace
  bats
  bazel
  bbmap
  bcftools
  bcl2fastq2
  bedops
  bedtools
  berkeleygw
  bioawk
  biobambam2
  bionano_tools
  biopython
  biotoolbox
  bismark
  blast+
  blender
  boost
  boost-compiled
  bowtie
  bowtie2
  braker2
  breseq
  busco
  bwa
  bwtool
  byobu
  bzip2
  cactus
  cadence
  caffe
  calibre
  canu
  cap3
  caper
  cellphonedb
  cellranger
  cellranger-atac
  chapel
  checkm
  chroma
  circos
  ciscall
  cite-seq-count
  clang
  clark
  clc-assembly-cell
  clinker
  clinqc
  cmake
  cnvkit
  cnvnator
  control-freec
  cosmosscope
  cp2k
  cpat
  crimap
  cromwell
  ctpnet
  cuba
  cuda
  cufflinks
  curl
  custom_waveview
  customsim
  cutadapt
  cutruntools
  cytoscape
  damask
  danpos2
  dapars
  datalad
  dcm2niix
  deepbinner
  deeplabcut
  deeptools
  deepvariant
  defuse
  degnorm
  delly
  detonate
  deviceQuery
  diamond
  discovardenovo
  dms_tools2
  doxygen
  drop-seq
  dsi-studio
  dx-toolkit
  dynare
  eagle
  eclipidrmergepeaks
  edirect
  eigen
  emboss
  epacts
  f-seq
  fabtests
  fastp
  fastq_pair
  fastq_screen
  fastqc
  fasttree
  fastx-toolkit
  fdtd
  febio
  fftw
  fhiaims
  finesim
  fitsio
  flashpca
  flex
  flye
  fontconfig
  fqtrim
  freebayes
  freefem
  freesurfer
  fsl
  fsleyes
  fsps
  fusion-inspector
  fusioncatcher
  gamess
  gatb
  gatk
  gaussian
  gcc
  gdal
  gdc-tsv-tool
  gdrcopy
  genrich
  geos
  gfold
  ghostscript
  gistic
  git
  glimmer
  glpk
  gmap-gsnap
  gmsh
  gnuplot
  go
  google-cloud-sdk
  googletest
  gossamer
  gpaw
  grace
  graphviz
  gromacs
  gsl
  gulp
  guppy
  gurobi
  hclust
  hdf5
  hifive
  hisat2
  hmmer
  homer
  hpl
  hspice
  htseq
  htslib
  humann2
  hydra
  hypre
  icount
  idp
  idp-fusion
  idr
  igv
  imagej
  imagemagick
  indrops
  infercnv
  inspector
  intel
  intel-mpi
  ipyrad
  itk
  jaaba
  jags
  java
  jdftx
  jellyfish
  jmol
  joe
  julia
  kaldi
  kallisto
  kentutils
  kite
  kneaddata
  kpp
  kraken2
  krona
  lammps
  lapack
  ldpred
  libevent
  libfabric
  libfaketime
  libgtextutils
  libjpeg
  libpng
  libxc
  libxml2
  lightgbm
  lncfuntk
  lohhla
  loomr
  luarocks
  macs
  magicblast
  magma
  malt
  mapsplice2
  mathematica
  matlab
  matlab-mcr
  maven
  medea
  meerkat
  megahit
  meme
  merlin
  metabat2
  metis
  mgltools
  minimac4
  mira
  mirdeep2
  mirge
  miso
  mixcr
  mkl
  mmseqs2
  modelsim
  molden
  molecularGSM
  molpro
  mongodb
  mopac
  mosek
  mpich
  mrtrix
  mrtrix3
  multinest
  multiqc
  mummer
  muscle
  mutsig
  namd
  nano
  nanoplot
  nauty
  nektar
  nektar++
  neovim
  netcdf
  neuron
  nextflow
  nextgenmap
  nfcore
  ngmerge
  ngsplot
  ngsqc
  nodejs
  novocraft
  nucleoatac
  nvshmem
  openbabel
  opencv
  openfoam
  openmpi
  optitype
  orca
  osss-ucx
  ovito
  p7zip
  packmol
  paml
  pandoc
  parallel
  paraview
  parmetis
  parsplice
  pcre
  peakdeck
  peakseq
  peaksplitter
  pedcheck
  perl
  petsc
  petsc-gcc
  pgi
  phast
  phylip
  phyloacc
  picard
  pilon
  pindel
  piranha
  pizzly
  plink
  plinkseq
  plumed
  pmix
  poppler
  porechop
  povray
  primer3
  prinseq
  proj
  proovread
  provirus
  psi4
  pureclip
  pvactools
  pybedtools
  pyscenic
  python
  pytorch
  qapa
  qchem
  qiime2
  qorts
  qt
  qualimap
  quantumespresso
  quast
  quickmirseq
  r
  racon
  radia
  rapsearch
  raxml-ng
  rdkit
  readtools
  reforge
  rgt
  rna-seqc
  rnachipintegrator
  rnacocktail
  rnaseqmut
  rosetta
  rsem
  rseqc
  rstudio
  rtg-core
  salmon
  sambamba
  samblaster
  samstat
  samtools
  sas
  scala
  scanpy
  scats
  scbayes
  seqspark
  seqtk
  sicer
  siesta
  singularity
  slurm
  smoove
  snakemake
  snap-aligner
  snpeff
  snptest
  snver
  snvmix2
  soapindel
  solar
  sortmerna
  sox
  spades
  spark
  sparrow
  spreg
  squid
  sra-toolkit
  srnanalyzer
  star
  star-fusion
  stata
  strelka
  stringtie
  stubb
  subread
  surfaceGSM
  svaba
  svdetect
  svviz2
  synopsys
  taiji
  taiji-view
  teaching
  telescope
  tensorflow
  texlive
  tinker
  tmux
  tophat
  torch
  tracer
  transdecoder
  trilinos
  trimgalore
  trimmomatic
  trinity
  trust
  trust4
  turbomole
  ucx
  uintah
  umi-tools
  unceqr
  valgrind
  vardictjava
  varscan
  vasp
  vasp-vtst
  vcf2maf
  vcflib
  vcftools
  vdjtools
  velocyto
  velvet
  venv
  vep
  vfs
  vim
  virus_detection_sra
  virusfinder
  virvarseq
  visit
  vlsi
  vmd
  vtk
  vtune
  vvp
  westpa
  xhmm
  xilinx/containers
  xilinx/sdx
  xilinx/vitis
  xilinx/vivado
  xtb
  xz
  zlib
  zoltan