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