BioHPC Cloud:
: User Guide

BioHPC Cloud Software

There are 1356 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, 7zip, a5, ABRicate, ABruijn, ABySS, AdapterRemoval, adephylo, Admixtools, Admixture, AF_unmasked, AFProfile, AFsample2, AGAT, agrep, albacore, Alder, AliTV-Perl interface, AlleleSeq, ALLMAPS, ALLPATHS-LG, alphafast, Alphafold, Alphafold3, alphapickle, Alphapulldown, AlphScore, Amber, AMOS, AMPHORA, amplicon.py, AMRFinder, AMRplusplus, analysis, ANGSD, AnnotaPipeline, Annovar, ant, antiSMASH, ANTs, anvio, apollo, arcs, ARGweaver, aria2, ariba, ARIES, Arlequin, ART, ASEQ, aspera, assembly-stats, aster, ASTRAL, atac-seq-pipeline, ataqv, athena_meta, ATLAS, Atlas-Link, ATLAS_GapFill, atom, ATSAS, Augustus, autocycler, AWS command line interface, AWS v2 Command Line Interface, axe, axel, BA3, BactSNP, bakta, BAMdash, bamm, bamsnap, bamsurgeon, bamtools, bamUtil, barcode_splitter, BarNone, Basset, BayeScan, Bayescenv, bayesR, baypass, bazel, BBMap/BBTools, bcalm, 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, bioinfo-notebook, biom-format, BioPerl, BioPython, Birdsuite, biscuit, Bismark, Blackbird, blasr, BLAST, BLAST_to_BED, blast2go, BLAT, BlobToolKit, BLUPF90, BMGE, bmtagger, boltz, bonito, Boost, Bowtie, Bowtie2, BPGA, bpnet-lite, Bracken, BRAKER, BRAT-NextGen, BRBseqTools, BreedingSchemeLanguage, breseq, brisktyper, brocc, BSBolt, bsmap, BSseeker2, btyper3, bubblewrap, BUSCO, BUSCO Phylogenomics, BWA, bwa-mem2, bwa-meth, bwtool, cactus, CAFE, CAFE5, caffe, cagee, canu, Canvas, CAP3, caper, CarveMe, CAT, catastrophy, catch, cBar, CBSU RNAseq, CCMetagen, CCTpack, cd-hit, cdbfasta, cdo, CEGMA, CellRanger, cellranger-arc, cellranger-atac, cellranger-dna, cellsnp-lite, centrifuge, centrifuger, centroFlye, CFM-ID, CFSAN SNP pipeline, CGAT, CheckM, CheckM2, chimera, ChimeraTE, chimerax, chip-seq-pipeline, chromeister, ChromHMM, chromosomer, Circlator, Circos, Circuitscape, CITE-seq-Count, clam, claude code, Claude Science, ClermonTyping, CLImATHET, clues, CLUMPP, clust, Clustal Omega, CLUSTALW, Cluster, cmake, CMSeq, cNMF, CNVnator, codex, coidb, coinfinder, colabfold, COLMAP, CombFold, Comparative-Annotation-Toolkit, compat, CONCOCT, Conda, Conform-gt, conpair, Cooler, coolpuppy, cooltools, copyNumberDiff, cortex_var, CoverM, crabs, CRISPRCasFinder, CRISPResso, crispron, Cromwell, CrossMap, CRT, CSP2, csubst, cuda, Cufflinks, curatedMetagenomicDataTerminal, cutadapt, cuteFC, cuteSV, Cytoscape, czid, dadi, dadi-1.6.3_modif, dadi-cli, danpos, DAS_Tool, dashing, DBSCAN-SWA, dDocent, DeconSeq, Deepbinner, deeplasmid, DeepTE, deepTools, Deepvariant, defusion, degenotate, delly, DESMAN, destruct, DETONATE, dfast, diamond, dipcall, diploSHIC, discoal, Discovar, Discovar de novo, distiller, distruct, DiTASiC, DIYABC, dmtcp, dnmtools, Docker, dorado, DRAM, dREG, dREG.HD, drep, Drop-seq, dropEst, dropSeqPipe, dsk, dssat, Dsuite, dTOX, duphold, DWGSIM, dynare, ea-utils, EagleC, earlgrey, ecCodes, ecopcr, ecoPrimers, ectyper, EDGE, edirect, EDTA, eems, EgaCryptor, EGAD, egapx, eggnog-mapper, EIGENSOFT, elai, ElMaven, emacs, EMBLmyGFF3, EMBOSS, EMIRGE, Empress, emu, 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, FASTK, 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, FEELnc, feems, feh, FFmpeg, fgbio, ficle, figaro, Fiji, Filtlong, fineRADstructure, fineSTRUCTURE, FIt-SNE, FlaGs2, FLAME-python, flash, flash2, flexbar, Flexible Adapter Remover, flexidot, Flye, FMAP, foldmason, foldseek, foundry, FragGeneScan, FragGeneScan, FragPipe, FRANz, freebayes, FSA, funannotate, FunGene Pipeline, FunOMIC, G-PhoCS, g4predict, GADMA, GAEMR, Galaxy, Galaxy in Docker, garlic, GATK, gatk4, gatk4amplicon.py, gblastn, Gblocks, GBRS, gbsx, gcc, GCTA, GDAL, gdc-client, gem, GEM library, GEMMA, GeMoMa, GENECONV, geneid, GeneMark, GeneRax, Genespace, GenoFLU, genomad, Genome STRiP, Genome Workbench, GenomeMapper, Genomescope, GenomeThreader, genometools, GenomicConsensus, genozip, gensim, GEOS, germline, gerp++, GET_PHYLOMARKERS, GetOrganelle, gfastats, gfaviz, GffCompare, gffread, giggle, gingr, git, glactools, GlimmerHMM, GLIMPSE, GLnexus, Globus connect personal, GMAP/GSNAP, gmx_MMPBSA, GNU Compilers, GNU parallel, go-perl, GO2MSIG, GONE, GoShifter, gradle, GraffiTE, 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, HapHiC, HaploMerger, Haplomerger2, haplostrips, HaploSync, happ, HapSeq2, harpy, HarvestTools, haslr, hdf5, helixer, hget, hh-suite, HiC-Pro, hic_qc, HiCExplorer, hicstuff, HiFiAdapterFilt, hifiasm, hificnv, HiPhase, HISAT2, HMMER, Homer, HOTSPOT, HTSeq, htslib, https://github.com/CVUA-RRW/RRW-PrimerBLAST, https://github.com/ksahlin/strobealign, huggingface-hub, hugin, humann, HUMAnN2, hybpiper, hyde, 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, IRMA, isoseq, itsx, iva, ivar, JaBbA, jags, Jane, java, jbrowse, JCVI, jellyfish, jsalignon/cactus, juicer, julia, jupyter, jupyterlab, kaiju, kallisto, Kent Utilities, keras, khmer, kineticsTools, kinfin, king, kma, KMC, KmerFinder, KmerGenie, kneaddata, kraken, KrakenTools, KronaTools, kSNP, kWIP, LACHESIS, lammps, LAPACK, lapels, LAST, lastz, lcMLkin, LDAK, LDBlockShow, LDhat, LeafCutter, leeHom, lefse, lep-anchor, Lep-MAP3, LEVIATHAN, lftp, Liftoff, lifton, ligandmpnn, Lighter, LinkedSV, LINKS, localcolabfold, LocARNA, LocusZoom, lofreq, longcallR, longcallR-nn, longqc, 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, majiq, MAKER, manta, mapDamage, mapquik, MAQ, MARS, MASH, mashtree, Mashtree, MaSuRCA, MATLAB, Matlab_runtime, Mauve, MaxBin, MaxQuant, McClintock, mccortex, MCHelper, mcl, MCscan, MCScanX, mdust, medaka, medusa, medusa2, megahit, MeGAMerge, MEGAN, meirlop, MELT, MEME Suite, MERLIN, merqury, meryl, MetaBAT, MetaBinner, MetaboAnalystR, MetaCache, MetaCRAST, metaCRISPR, metamaps, MetAMOS, MetaPathways, MetaPhlAn, metapop, metaron, MetaVelvet, MetaVelvet-SL, metaWRAP, methbat, methpipe, methylasso, mfeprimer, MGmapper, MicrobeAnnotator, microtrait, MIDAS, MiFish, Migrate-n, mikado, MinCED, minigraph, Minimac3, Minimac4, minimap2, miniprot, mira, miRDeep2, mirge3, miRquant, MISO, MITE-Hunter, MITE-Tracker, MITObim, MitoFinder, mitohelper, MitoHiFi, mity, MiXCR, MixMapper, MKTest, mlift, MLNe, mlst, MMAP, MMSEQ, MMseqs2, MMTK, MobileElementFinder, ModDotPlot, modeltest, MODIStsp-2.0.5, module, moments, momi, MoMI-G, mongo, mono, monocle3, morphographx, 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, NanoLyse, NanoPlot, Nanopolish, nanovar, ncbi_datasets, ncftp, ncl, NECAT, Nemo, Netbeans, NEURON, new_fugue, Nextflow, NextGenMap, NextPolish2, nf-core, nf-core/rnaseq, nf-LO, ngmlr, NGS_data_processing, NGSadmix, ngsDist, ngsF, ngsLD, NGSNGS, ngsplot, NgsRelate, ngsTools, NGSUtils, NINJA, NLR-Annotator, NLR-Parser, NLRtracker, Novoalign, NovoalignCS, nQuire, NRSA, ntSynt, nucMACC, NuDup, numactl, nvidia-docker, nvtop, Oases, OBITools, Octave, odgi, OMA, Oneflux, OpenBLAS, openmpi, openslide, openssl, ORFeus, ORFfinder, orthodb-clades, OrthoFinder, orthologr, Orthomcl, osfclient, pacbio, PacBioTestData, PAGIT, pairtools, pal2nal, paleomix, PAML, panacus, panaroo, pandas, pandaseq, pandoc, pangene, pankmer, PanPhlAn, PanPhlAn_pangenome_exporter, Panseq, pantools, paPAML, Parsnp, PASA, PASTEC, PAUP*, pauvre, pb-assembly, pb-CpG-tools, pbalign, pbbam, pbh5tools, PBJelly, pblat, pbmm2, pbpigeon, PBSuite, pbsv, pbtk, PCAngsd, pcre, pcre2, PeakRanger, peaks2utr, PeakSplitter, PEAR, PEER, PennCNV, peppro, PERL, PfamScan, pgap, PGDSpider, ph5tools, Phage_Finder, pharokka, phasedibd, PHAST, phenopath, PhiSpy, Phobius, PHRAPL, phykit, PHYLIP, PhyloCSF, phyloFlash, phylonet, phylophlan*, PhyloPhlAn2, phylophlan3, phyluce, PhyML, phyx, Picard, PICRUSt2, pigz, Pilon, Pindel, piPipes, PIQ, piranha, 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, prodigy, progenomics, progressiveCactus, PROJ, prokka, Proseq2, ProteinMPNN, proteowizard, 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, q2-picrust2, qapa, qcat, QIIME, QIIME2, QTCAT, Quake, Qualimap, QuantiSNP2, quarTeT, 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, readtagger, REAGO, REAPR, Rebaler, reCOGnizer, Red, ReferenceSeeker, regenie, regtools, REINDEER, Relate, relion, RelocaTE2, Repbase, RepeatMasker, RepeatModeler, RERconverge, ReSeq, resistify, RevBayes, RFdiffusion, RFDpoly, RFMix, RGAAT, rgdal, RGI, Rgtsvm, Ribotaper, ripgrep, rJava, rMATS, RNAMMER, rnaQUAST, Rnightlights, roadies, Roary, Rockhopper, rohan, RoseTTAFold-All-Atom, RoseTTAFold2, RoseTTAFold2NA, rphast, RpsbProc, Rqtl, Rqtl2, RSAT, rseg, RSEM, RSeQC, RStudio, rtfbs_db, ruby, run_dbcan, rust, rv-tdt, sabre, SaguaroGW, salmon, SALSA, Sambamba, samblaster, sample, SampleTracker, samplot, samtabix, Samtools, Satsuma, Satsuma2, sawfish, SCALE, scanorama, SCE-VCF, scikit-learn, Scoary, scoary-2, SCOTCH, scTE, scythe, seaborn, SEACR, SecretomeP, segul, self-assembling-manifold, selscan, seqfu, seqkit, SeqPrep, SeqSero2, seqtk, SequelTools, sequenceTubeMap, Seurat, sf, sgrep, sgrep sorted_grep, SHAPEIT, SHAPEIT4, SHAPEIT5, shasta, Shiny, shoelaces, shore, SHOREmap, shortBRED, SHRiMP, SICER2, sickle, sift4g, SignalP, SimPhy, simsapiper, simuPOP, simuscop, sina, SINGER, singularity, sinto, sirius, sistr_cmd, skani, skera, SKESA, skewer, slamdunk, SLiM, SLURM, smap, smash, smcpp, smoove, SMRT Analysis, SMRT LINK, smudgeplot, 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, sourmash, spaceranger, SPAdes, SPALN, SparCC, sparsehash, SPARTA, SpeciesDetector, 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, swarm, sweed, SweepFinder, SweepFinder2, sweepsims, swiss2fasta.py, sword, syri, tabix, TAGADA, tagdust, Taiji, tama, Tandem Repeats Finder (TRF), tardis, TargetP, TASSEL 3, TASSEL 4, TASSEL 5, tax_myPHAGE, tbl2asn, tcoffee, TE-Aid, TEFLoN, telescope, TELR, TEMP2, TensorFlow, TEToolkit, TEtranscripts, texlive, TFEA, tfmodisco, 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, twisst2, UBCG2, ullar, ultra, ultraplex, UMAP, UMI-tools, umi-transfer, UMIScripts, Unicycler, UniRep, unitig-caller, unrar, usearch, VALET, valor, vamb, VAPiD, variabel, Variant Effect Predictor, VarScan, VCF-kit, vcf2diploid, VCF2PCACluster, vcf2phylip, vcfCooker, vcflib, vcftools, vdjtools, Velvet, vep, verkko, VESPA, vg, VIBRANT, Vicuna, ViennaRNA, VIP, viral-ngs, virmap, VirSorter, VirusDetect, VirusFinder 2, visidata, vispr, VizBin, vmatch, vscode, vsearch, vSNP3, vt, WASP, webin-cli, wget, wgs-assembler (Celera), WGSassign, What_the_Phage, whatshap, wiggletools, windowmasker, wine, Winnowmap, Wise2 (Genewise), wombat, Xander_assembler, xpclr, yaha, yahs, yap

Details for alphafast (If the copy-pasted commands do not work, use this tool to remove unwanted characters)

mkdir /workdir/$USER
cd /workdir/$USER

git clone https://github.com/RomeroLab/alphafast.git
apptainer build alphafast.sif docker://romerolabduke/alphafast:latest

mkdir /workdir/$USER/alphafastdbs

tar -xzf /home2/shared/alphafast/mmcif_files.tar.gz -C /workdir/qisun/alphafastdbs

tar -xf /home2/shared/alphafast/mmseqs.tar -C /workdir/qisun/alphafastdbs

mkdir /workdir/$USER/alphafast_tmp
mkdir /workdir/$USER/alphafast_jax_cache  
cd /workdir/$USER/alphafast
./scripts/run_alphafast.sh 
    --backend singularity 
    --container /workdir/$USER/alphafast.sif 
    --input_dir /path/to/inputs 
    --output_dir /path/to/outputs 
    --db_dir /workdir/$USER/alphafastdbs 
    --weights_dir /path/to/weights 
    --temp_dir /workdir/$USER/alphafast_tmp 
    --jax_compilation_cache_dir /workdir/$USER/alphafast_jax_cache