BioHPC Cloud Software
There are 1298 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, Alphafold, Alphafold3, alphapickle, Alphapulldown, AlphScore, Amber, AMOS, AMPHORA, amplicon.py, AMRFinder, AMRplusplus, analysis, ANGSD, AnnotaPipeline, Annovar, ant, antiSMASH, anvio, apollo, arcs, ARGweaver, aria2, ariba, 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, 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, brisktyper, 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, centrifuger, centroFlye, CFM-ID, CFSAN SNP pipeline, CheckM, CheckM2, chimera, ChimeraTE, chimerax, chip-seq-pipeline, chromeister, ChromHMM, chromosomer, Circlator, Circos, Circuitscape, CITE-seq-Count, clam, ClermonTyping, CLImATHET, clues, CLUMPP, clust, Clustal Omega, CLUSTALW, Cluster, cmake, CMSeq, CNVnator, coidb, coinfinder, colabfold, COLMAP, CombFold, Comparative-Annotation-Toolkit, compat, CONCOCT, Conda, Conform-gt, Cooler, coolpuppy, cooltools, copyNumberDiff, cortex_var, CoverM, crabs, CRISPRCasFinder, CRISPResso, crispron, Cromwell, CrossMap, CRT, CSP2, cuda, Cufflinks, curatedMetagenomicDataTerminal, cutadapt, cuteFC, cuteSV, Cytoscape, 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, 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, flash, flash2, flexbar, Flexible Adapter Remover, flexidot, Flye, FMAP, FragGeneScan, FragGeneScan, FRANz, freebayes, FSA, funannotate, FunGene Pipeline, FunOMIC, G-PhoCS, g4predict, GADMA, GAEMR, Galaxy, Galaxy in Docker, garlic, GATK, gatk4, gatk4amplicon.py, gblastn, Gblocks, GBRS, 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, 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, HaploMerger, Haplomerger2, haplostrips, HaploSync, happ, HapSeq2, harpy, HarvestTools, haslr, hdf5, helixer, hget, hh-suite, HiC-Pro, hic_qc, HiCExplorer, HiFiAdapterFilt, hifiasm, hificnv, HiPhase, HISAT2, HMMER, Homer, HOTSPOT, HTSeq, htslib, https://github.com/CVUA-RRW/RRW-PrimerBLAST, https://github.com/ksahlin/strobealign, 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, 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, majiq, MAKER, manta, mapDamage, mapquik, MAQ, MARS, MASH, mashtree, Mashtree, MaSuRCA, MATLAB, Matlab_runtime, Mauve, MaxBin, MaxQuant, McClintock, mccortex, mcl, MCscan, MCScanX, mdust, medaka, medusa, medusa2, megahit, MeGAMerge, MEGAN, 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, 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, NanoPlot, Nanopolish, nanovar, ncbi_datasets, ncftp, ncl, NECAT, Nemo, Netbeans, NEURON, new_fugue, Nextflow, NextGenMap, NextPolish2, nf-core, nf-core/rnaseq, ngmlr, NGS_data_processing, NGSadmix, ngsDist, ngsF, ngsLD, NGSNGS, ngsplot, NgsRelate, ngsTools, NGSUtils, NINJA, NLR-Annotator, NLR-Parser, NLRtracker, Novoalign, NovoalignCS, nQuire, NRSA, ntSynt, NuDup, numactl, nvidia-docker, nvtop, Oases, OBITools, Octave, odgi, OMA, Oneflux, OpenBLAS, openmpi, openslide, openssl, ORFeus, 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, PBSuite, pbsv, pbtk, PCAngsd, pcre, pcre2, PeakRanger, peaks2utr, PeakSplitter, PEAR, PEER, PennCNV, peppro, PERL, PfamScan, pgap, PGDSpider, ph5tools, Phage_Finder, pharokka, phasedibd, PHAST, phenopath, 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, 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, readtagger, REAGO, REAPR, Rebaler, reCOGnizer, Red, ReferenceSeeker, regenie, regtools, Relate, relion, 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, rseg, RSEM, RSeQC, RStudio, rtfbs_db, ruby, run_dbcan, 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, 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, SKESA, skewer, 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, 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, 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, VCF2PCACluster, vcf2phylip, vcfCooker, vcflib, vcftools, vdjtools, Velvet, vep, verkko, VESPA, vg, 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 Basset (If the copy-pasted commands do not work, use this tool to remove unwanted characters)
| Name: | Basset |
| Version: | 0.1.0 |
| OS: | Linux |
| About: | Deep convolutional neural networks for DNA sequence analysis. |
| Added: | 5/15/2017 9:55:07 PM |
| Updated: | |
| Link: | https://github.com/davek44/Basset |
| Notes: | ## verified to works on cbsugpu03, if it doesnot work on your machine, follow the second part of the instruction to install by yourself
## set environment for cuda torch and basset
export PATH=/usr/local/cuda/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
. /programs/torch/install/bin/torch-activate
export BASSETDIR=/programs/Basset
export PATH=$BASSETDIR/src:$PATH
export PYTHONPATH=$BASSETDIR/src:$PYTHONPATH
export LUA_PATH="$BASSETDIR/src/?.lua;$LUA_PATH"
## to run the software, use the command directly, and use -cuda command if you want to use GPU
e.g.
basset_train.lua -cuda -job myparams.txt -save mycnn.h5
## if the previous instructions does not work, follow the instructions below to install torch and Basset by yourself
git clone https://github.com/torch/distro.git ~/torch --recursive
cd ~/torch
export PATH=/usr/local/cuda-8.0/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda/lib64
export TORCH_NVCC_FLAGS="-D__CUDA_NO_HALF_OPERATORS__"
./install.sh
source ~/torch/install/bin/torch-activate
cd $HOME
git clone https://github.com/davek44/Basset.git
cd Basset
export BASSETDIR=/programs/Basset
export PATH=$BASSETDIR/src:$PATH
export PYTHONPATH=$BASSETDIR/src:$PYTHONPATH
export LUA_PATH="$BASSETDIR/src/?.lua;$LUA_PATH"
./install_dependencies.py
# to run your own installation:
export PATH=/usr/local/cuda/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
source ~/torch/install/bin/torch-activate
export BASSETDIR=$HOME/Basset
export PATH=$BASSETDIR/src:$PATH
export PYTHONPATH=$BASSETDIR/src:$PYTHONPATH
export LUA_PATH="$BASSETDIR/src/?.lua;$LUA_PATH"
basset_train.lua -cuda -job myparams.txt -save mycnn.h5
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