BioHPC Cloud Software
There are 1204 software titles installed in BioHPC Cloud. The sofware is available on all machines (unless stated otherwise in notes), complete list of programs is below, please click on a title to see details and instructions. Tabular list of software is available here
Please read details and instructions before running any program, it may contain important information on how to properly use the software in BioHPC Cloud.
3D Slicer, 3d-dna, 454 gsAssembler or gsMapper, a5, ABRicate, ABruijn, ABySS, AdapterRemoval, adephylo, Admixtools, Admixture, AF_unmasked, AFProfile, AGAT, agrep, albacore, Alder, AliTV-Perl interface, AlleleSeq, ALLMAPS, ALLPATHS-LG, Alphafold, alphapickle, Alphapulldown, AlphScore, AMOS, AMPHORA, amplicon.py, AMRFinder, analysis, ANGSD, AnnotaPipeline, Annovar, ant, antiSMASH, anvio, apollo, arcs, ARGweaver, aria2, ariba, Arlequin, ART, ASEQ, aspera, assembly-stats, ASTRAL, atac-seq-pipeline, ataqv, athena_meta, ATLAS, Atlas-Link, ATLAS_GapFill, atom, ATSAS, Augustus, AWS command line interface, AWS v2 Command Line Interface, axe, axel, BA3, BactSNP, bakta, bamsnap, bamsurgeon, bamtools, bamUtil, barcode_splitter, BarNone, Basset, BayeScan, Bayescenv, bayesR, baypass, bazel, BBMap/BBTools, BCFtools, BCL convert, bcl2fastq, BCP, bdbag, Beagle, beagle-lib, BEAST, BEAST X, Beast2, bed2diffs, bedops, BEDtools, bettercallsal, bfc, bgc, bgen, bicycle, BiG-SCAPE, bigQF, bigtools, bigWig, bioawk, biobakery, biobambam, Bioconductor, biom-format, BioPerl, BioPython, Birdsuite, biscuit, Bismark, Blackbird, blasr, BLAST, BLAST_to_BED, blast2go, BLAT, BlobToolKit, BLUPF90, BMGE, bmtagger, bonito, Boost, Bowtie, Bowtie2, BPGA, Bracken, BRAKER, BRAT-NextGen, BRBseqTools, BreedingSchemeLanguage, breseq, brocc, BSBolt, bsmap, BSseeker2, btyper3, BUSCO, BUSCO Phylogenomics, BWA, bwa-mem2, bwa-meth, bwtool, cactus, CAFE, CAFE5, caffe, cagee, canu, Canvas, CAP3, caper, CarveMe, catch, cBar, CBSU RNAseq, CCMetagen, CCTpack, cd-hit, cdbfasta, cdo, CEGMA, CellRanger, cellranger-arc, cellranger-atac, cellranger-dna, centrifuge, centroFlye, CFM-ID, CFSAN SNP pipeline, CheckM, CheckM2, chimera, ChimeraTE, chimerax, chip-seq-pipeline, chromosomer, Circlator, Circos, Circuitscape, CITE-seq-Count, ClermonTyping, clues, CLUMPP, clust, Clustal Omega, CLUSTALW, Cluster, cmake, CMSeq, CNVnator, coinfinder, colabfold, CombFold, Comparative-Annotation-Toolkit, compat, CONCOCT, Conda, Cooler, copyNumberDiff, cortex_var, CoverM, crabs, CRISPRCasFinder, CRISPResso, crispron, Cromwell, CrossMap, CRT, cuda, Cufflinks, curatedMetagenomicDataTerminal, cutadapt, cuteSV, Cytoscape, dadi, dadi-1.6.3_modif, dadi-cli, danpos, DAS_Tool, dashing, DBSCAN-SWA, dDocent, DeconSeq, Deepbinner, deeplasmid, DeepTE, deepTools, Deepvariant, defusion, delly, DESMAN, destruct, DETONATE, dfast, diamond, dipcall, diploSHIC, discoal, Discovar, Discovar de novo, distruct, DiTASiC, DIYABC, dnmtools, Docker, dorado, DRAM, dREG, dREG.HD, drep, Drop-seq, dropEst, dropSeqPipe, dsk, dssat, Dsuite, dTOX, duphold, DWGSIM, dynare, ea-utils, earlgrey, ecCodes, ecopcr, ecoPrimers, ectyper, EDGE, edirect, EDTA, eems, EgaCryptor, EGAD, eggnog-mapper, EIGENSOFT, elai, ElMaven, EMBLmyGFF3, EMBOSS, EMIRGE, Empress, enfuse, EnTAP, entropy, epa-ng, ephem, epic2, ermineJ, ete3, EukDetect, EukRep, EVE, EVM, exabayes, exonerate, ExpansionHunterDenovo-v0.8.0, eXpress, FALCON, FALCON_unzip, Fast-GBS, fasta, FastAAI, FastANI, fastcluster, fastGEAR, FastME, FastML, fastp, FastQ Screen, fastq-multx-1.4.3, fastq_demux, fastq_pair, fastq_species_detector, FastQC, fastqsplitter, fastsimcoal2, fastspar, fastStructure, FastTree, FASTX, fcs, feems, feh, FFmpeg, fgbio, ficle, figaro, Fiji, Filtlong, fineRADstructure, fineSTRUCTURE, FIt-SNE, FlaGs2, flash, flash2, flexbar, Flexible Adapter Remover, Flye, FMAP, FragGeneScan, FragGeneScan, FRANz, freebayes, FSA, funannotate, FunGene Pipeline, FunOMIC, G-PhoCS, GADMA, GAEMR, Galaxy, Galaxy in Docker, GATK, gatk4, gatk4amplicon.py, gblastn, Gblocks, GBRS, gcc, GCTA, GDAL, gdc-client, GEM library, GEMMA, GeMoMa, GENECONV, geneid, GeneMark, GeneRax, Genespace, genomad, Genome STRiP, Genome Workbench, GenomeMapper, Genomescope, GenomeThreader, genometools, GenomicConsensus, genozip, gensim, GEOS, germline, gerp++, GET_PHYLOMARKERS, gfaviz, GffCompare, gffread, giggle, git, glactools, GlimmerHMM, GLIMPSE, GLnexus, Globus connect personal, GMAP/GSNAP, gmx_MMPBSA, GNU Compilers, GNU parallel, go-perl, GO2MSIG, GONE, GoShifter, gradle, graftM, grammy, GraPhlAn, graphtyper, graphviz, greenhill, GRiD, gridss, Grinder, grocsvs, GROMACS, GroopM, GSEA, gsort, GTDB-Tk, GTFtools, Gubbins, gunc, GUPPY, gvcftools, hail, hal, HapCompass, HAPCUT, HAPCUT2, hapflk, HaploMerger, Haplomerger2, haplostrips, HaploSync, HapSeq2, harpy, HarvestTools, haslr, hdf5, helixer, hget, hh-suite, HiC-Pro, hic_qc, HiCExplorer, HiFiAdapterFilt, hifiasm, hificnv, HISAT2, HMMER, Homer, HOTSPOT, HTSeq, htslib, https://github.com/CVUA-RRW/RRW-PrimerBLAST, hugin, humann, HUMAnN2, hybpiper, HyLiTE, Hyper-Gen, hyperopt, HyPhy, hyphy-analyses, iAssembler, IBDLD, IBDNe, IBDseq, idba, IDBA-UD, idemux, IDP-denovo, idr, idseq, IgBLAST, IGoR, IGV, IMa2, IMa2p, IMAGE, ImageJ, ImageMagick, Immcantation, impute2, impute5, IMSA-A, INDELseek, infernal, Infomap, inspector, inStrain, inStrain_lite, InStruct, Intel MKL, InteMAP, InterProScan, ipyrad, IQ-TREE, iRep, isoseq, JaBbA, jags, Jane, java, jbrowse, JCVI, jellyfish, jsalignon/cactus, juicer, julia, jupyter, jupyterlab, kaiju, kallisto, Kent Utilities, keras, khmer, kinfin, king, kma, KMC, KmerFinder, KmerGenie, kneaddata, kraken, KrakenTools, KronaTools, kSNP, kWIP, LACHESIS, lammps, LAPACK, lapels, LAST, lastz, lcMLkin, LDAK, LDhat, LeafCutter, leeHom, lep-anchor, Lep-MAP3, LEVIATHAN, lftp, Liftoff, lifton, Lighter, LinkedSV, LINKS, localcolabfold, LocARNA, LocusZoom, lofreq, longranger, Loupe, LS-GKM, LTR_retriever, LUCY, LUCY2, LUMPY, lyve-SET, m6anet, Macaulay2, MACE, MACS, MaCS simulator, MACS2, macs3, maffilter, MAFFT, mafTools, MAGeCK, MAGeCK-VISPR, Magic-BLAST, magick, MAGScoT, MAKER, manta, mapDamage, mapquik, MAQ, MARS, MASH, mashtree, Mashtree, MaSuRCA, MATLAB, Matlab_runtime, Mauve, MaxBin, MaxQuant, McClintock, mccortex, mcl, MCscan, MCScanX, medaka, medusa, megahit, MeGAMerge, MEGAN, MELT, MEME Suite, MERLIN, merqury, MetaBAT, MetaBinner, MetaboAnalystR, MetaCache, MetaCRAST, metaCRISPR, metamaps, MetAMOS, MetaPathways, MetaPhlAn, metapop, metaron, MetaVelvet, MetaVelvet-SL, metaWRAP, methpipe, mfeprimer, MGmapper, MicrobeAnnotator, microtrait, MIDAS, MiFish, Migrate-n, mikado, MinCED, minigraph, Minimac3, Minimac4, minimap2, miniprot, mira, miRDeep2, mirge3, miRquant, MISO, MITObim, MitoFinder, mitohelper, MitoHiFi, mity, MiXCR, MixMapper, MKTest, mlift, mlst, MMAP, MMSEQ, MMseqs2, MMTK, MobileElementFinder, modeltest, MODIStsp-2.0.5, module, moments, momi, MoMI-G, mongo, mono, monocle3, mosdepth, mothur, MrBayes, mrcanavar, mrsFAST, msdial, msld, MSMC, msprime, MSR-CA Genome Assembler, msstats, MSTMap, mugsy, MultiQC, multiz-tba, MUMandCo, MUMmer, mummer2circos, muscle, MUSIC, Mutation-Simulator, muTect, myte, MZmine, nag-compiler, namfinder, nanocompore, nanofilt, NanoPlot, Nanopolish, nanovar, ncbi_datasets, ncftp, ncl, NECAT, Nemo, Netbeans, NEURON, new_fugue, Nextflow, NextGenMap, NextPolish2, nf-core/rnaseq, ngmlr, NGS_data_processing, NGSadmix, ngsDist, ngsF, ngsLD, NGSNGS, NgsRelate, ngsTools, NGSUtils, NINJA, NLR-Annotator, NLR-Parser, NLRtracker, Novoalign, NovoalignCS, nQuire, NRSA, NuDup, numactl, nvidia-docker, nvtop, Oases, OBITools, Octave, OMA, Oneflux, OpenBLAS, openmpi, openslide, openssl, ORFeus, orthodb-clades, OrthoFinder, orthologr, Orthomcl, pacbio, PacBioTestData, PAGIT, pairtools, pal2nal, paleomix, PAML, panacus, panaroo, pandas, pandaseq, pandoc, pangene, PanPhlAn, Panseq, pantools, Parsnp, PASA, PASTEC, PAUP*, pauvre, pb-assembly, pbalign, pbbam, pbh5tools, PBJelly, pblat, pbmm2, PBSuite, pbsv, pbtk, PCAngsd, pcre, pcre2, PeakRanger, PeakSplitter, PEAR, PEER, PennCNV, peppro, PERL, PfamScan, pgap, PGDSpider, ph5tools, Phage_Finder, pharokka, phasedibd, PHAST, phenopath, Phobius, PHRAPL, PHYLIP, PhyloCSF, phyloFlash, phylophlan*, PhyloPhlAn2, phylophlan3, phyluce, PhyML, phyx, Picard, PICRUSt2, pigz, Pilon, Pindel, piPipes, PIQ, pixy, PlasFlow, platanus, Platypus, plink, plink2, Plotly, plotsr, plumed, pocp, Point Cloud Library, popbam, PopCOGenT, PopLDdecay, Porechop, poretools, portcullis, POUTINE, pplacer, PRANK, preseq, pretext-suite, primalscheme, primer3, PrimerBLAST, PrimerPooler, prinseq, prodigal, progenomics, progressiveCactus, PROJ, prokka, Proseq2, ProtExcluder, protolite, PSASS, psmc, psutil, pullseq, purge_dups, pyani, PyCogent, pycoQC, pyfaidx, pyGenomeTracks, PyMC, pymol-open-source, pyopencl, pypy, pyRAD, pyrho, Pyro4, pyseer, PySnpTools, python, PyTorch, PyVCF, qapa, qcat, QIIME, QIIME2, QTCAT, Quake, Qualimap, QuantiSNP2, QUAST, quickmerge, QUMA, QuPath, R, RACA, racon, rad_haplotyper, RADIS, RadSex, RagTag, rapt, RAPTR-SV, RATT, raven, RAxML, raxml-ng, Ray, rck, rclone, Rcorrector, RDP Classifier, REAGO, REAPR, Rebaler, reCOGnizer, Red, ReferenceSeeker, regenie, regtools, Relate, RelocaTE2, Repbase, RepeatMasker, RepeatModeler, RERconverge, ReSeq, resistify, RevBayes, RFdiffusion, RFMix, RGAAT, rgdal, RGI, Rgtsvm, Ribotaper, ripgrep, rJava, rMATS, RNAMMER, rnaQUAST, Rnightlights, roadies, Roary, Rockhopper, rohan, RoseTTAFold-All-Atom, RoseTTAFold2NA, rphast, Rqtl, Rqtl2, RSAT, RSEM, RSeQC, RStudio, rtfbs_db, ruby, run_dbcan, sabre, SaguaroGW, salmon, SALSA, Sambamba, samblaster, sample, SampleTracker, samplot, samtabix, Samtools, Satsuma, Satsuma2, SCALE, scanorama, SCE-VCF, scikit-learn, Scoary, scoary-2, scTE, scythe, seaborn, SEACR, SecretomeP, segul, self-assembling-manifold, selscan, seqfu, seqkit, SeqPrep, seqtk, SequelTools, sequenceTubeMap, Seurat, sf, sgrep, sgrep sorted_grep, SHAPEIT, SHAPEIT4, SHAPEIT5, shasta, Shiny, shoelaces, shore, SHOREmap, shortBRED, SHRiMP, sickle, sift4g, SignalP, SimPhy, simuPOP, sina, SINGER, singularity, sinto, sirius, sistr_cmd, skani, SKESA, skewer, SLiM, SLURM, smap, smash, smcpp, smoove, SMRT Analysis, SMRT LINK, snakemake, snap, SnapATAC, snapatac2, SNAPP, SnapTools, snATAC, SNeP, Sniffles, snippy, snp-sites, snpArcher, SnpEff, SNPgenie, SNPhylo, SNPsplit, SNVPhyl, SOAP2, SOAPdenovo, SOAPdenovo-Trans, SOAPdenovo2, SoloTE, SomaticSniper, songbird, sorted_grep, spaceranger, SPAdes, SPALN, SparCC, sparsehash, SPARTA, speedseq, split-fasta, SQANTI3, sqlite, SqueezeMeta, SQuIRE, SRA Toolkit, srst2, ssantichaivekin/empress, stacks, Stacks 2, stairway-plot, stampy, STAR, staramr, Starcode, statmodels, stellarscope, STITCH, STPGA, StrainPhlAn, strawberry, Strelka, stringMLST, StringTie, STRUCTURE, Structure_threader, Struo2, stylegan2-ada-pytorch, subread, sumatra, supernova, suppa, SURPI, surpyvor, SURVIVOR, sutta, SV-plaudit, SVaBA, SVclone, SVDetect, svengine, SVseq2, svtools, svtyper, svviz2, SWAMP, sweed, SweepFinder, SweepFinder2, sweepsims, swiss2fasta.py, sword, syri, tabix, tagdust, Taiji, tama, Tandem Repeats Finder (TRF), tardis, TargetP, TASSEL 3, TASSEL 4, TASSEL 5, tax_myPHAGE, tbl2asn, tcoffee, TE-Aid, telescope, TensorFlow, TEToolkit, TEtranscripts, texlive, TFEA, tfTarget, thermonucleotideBLAST, ThermoRawFileParser, TMHMM, tmux, Tomahawk, TopHat, Torch, traitRate, Trans-Proteomic Pipeline (TPP), TransComb, TransDecoder, TRANSIT, transrate, TRAP, tree, treeCl, treemix, treePL, Trim Galore!, trimal, trimmomatic, Trinity, Trinotate, TrioCNV2, tRNAscan-SE, Trycycler, UBCG2, UCSC Kent utilities, ullar, ultra, ultraplex, UMAP, UMI-tools, umi-transfer, UMIScripts, Unicycler, UniRep, unitig-caller, unrar, usearch, VALET, valor, vamb, variabel, Variant Effect Predictor, VarScan, VCF-kit, vcf2diploid, vcf2phylip, vcfCooker, vcflib, vcftools, vdjtools, Velvet, vep, VESPA, vg, Vicuna, ViennaRNA, VIP, viral-ngs, virmap, VirSorter, VirusDetect, VirusFinder 2, visidata, vispr, VizBin, vmatch, vscode, vsearch, vt, WASP, webin-cli, wget, wgs-assembler (Celera), WGSassign, What_the_Phage, wiggletools, windowmasker, wine, Winnowmap, Wise2 (Genewise), wombat, Xander_assembler, xpclr, yaha, yahs, yap
Details for Cytoscape (If the copy-pasted commands do not work, use this tool to remove unwanted characters)
| Name: | Cytoscape |
| Version: | v3.10.2 |
| OS: | Linux |
| About: | An open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. |
| Added: | 8/26/2024 5:41:38 PM |
| Updated: | |
| Link: | https://cytoscape.org/what_is_cytoscape.html |
| Download: | https://cytoscape.org/download-platforms.html |
| Notes: | Cytoscape currently doea not run on GPU servers.
To run Cytoscape, you have to log in to a server in graphical mode (i.e., using either VNC or ssh with X11 forwarding; see https://biohpc.cornell.edu/lab/userguide.aspx?a=access#A5 for details).
Starting Cytoscape:
While logged in to the server, run the following commands:
export JAVA_HOME=/programs/jdk-17.0.10
/programs/Cytoscape_v3.10.2/cytoscape.sh
While the program is slaunching, you will notice two error messages starting with Unable to update instance pid... and java.lang.RuntimeException: OpenCL.. followed by a few lines of traceback. Both messages should be ignored. After a few seconds you should see the Cytoscape window open up.
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