BioHPC Cloud:
: User Guide

BioHPC Cloud Software

There are 1190 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, 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, 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, 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-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, 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, 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, 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, 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, SnpEff, SNPgenie, SNPhylo, SNPsplit, SNVPhyl, SOAP2, SOAPdenovo, SOAPdenovo-Trans, SOAPdenovo2, SoloTE, SomaticSniper, 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, 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, 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 miRquant (If the copy-pasted commands do not work, use this tool to remove unwanted characters)

mkdir -p /workdir/$USER/project1

cp -r /programs/miRquant-2.0/configuration /workdir/$USER/project1

#only modify the values for: genome, output, project, genome_release, species nad adapter. Do not change the values for "mirquant" and "shrimp path"

#replace the parts myUSERID and project1 

singularity shell -C --bind /workdir/$USER --bind /tmp /programs/miRquant-2.0/mirquant.sif

cd /miRquant

python miRquant.py /workdir/myUSERID/project1/configuration

python runC.py /workdir/myUSERID/project1/configuration

python process_summary_to_tab.py /workdir/myUSERID/project1/configuration

python final_processing.py /workdir/myUSERID/project1/configuration