BioHPC Cloud Software
There is 653 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.
454 gsAssembler or gsMapper, a5, ABRicate, ABruijn, ABySS, AdapterRemoval, adephylo, Admixtools, Admixture, agrep, albacore, Alder, AlleleSeq, ALLMAPS, ALLPATHS-LG, AMOS, AMPHORA, analysis, ANGSD, Annovar, antiSMASH, apollo, Arlequin, aspera, assembly-stats, atac-seq-pipeline, athena_meta, ATLAS, Atlas-Link, ATLAS_GapFill, ATSAS, Augustus, AWS command line interface, axe, BactSNP, bamtools, bamUtil, Basset, BayeScan, Bayescenv, BBmap, BCFtools, bcl2fastq, BCP, Beagle, Beast2, bedops, BEDtools, bfc, bgc, bgen, bigQF, bigWig, bioawk, biobambam, Bioconductor, biom-format, BioPerl, BioPython, Birdsuite, Bismark, blasr, BLAST, blast2go, BLAT, BLUPF90, BMGE, bmtagger, Boost, Bowtie, Bowtie2, BPGA, Bracken, BRAT-NextGen, BreedingSchemeLanguage, breseq, brocc, BSseeker2, BUSCO, BWA, bwa-meth, cactus, canu, CAP3, cBar, CBSU RNAseq, CCTpack, cd-hit, CEGMA, CellRanger, cellranger-atac, centrifuge, CFSAN SNP pipeline, CheckM, chimera, chromosomer, Circlator, Circos, Circuitscape, CLUMPP, Clustal Omega, CLUSTALW, Cluster, cmake, CNVnator, compat, CONCOCT, Conda, copyNumberDiff, cortex_var, CRISPRCasFinder, CRISPResso, CrossMap, CRT, cuda, Cufflinks, cutadapt, dadi, dadi-1.6.3_modif, danpos, dDocent, DeconSeq, deepTools, defusion, delly, destruct, DETONATE, diamond, diploSHIC, discoal, Discovar, Discovar de novo, distruct, DiTASiC, DIYABC, Docker, dREG, dREG.HD, Drop-seq, dropEst, dropSeqPipe, dsk, Dsuite, ea-utils, ecopcr, ecoPrimers, ectyper, EDGE, edirect, eems, EIGENSOFT, EMBOSS, entropy, ephem, epic2, ermineJ, ete3, exabayes, exonerate, eXpress, FALCON, FALCON_unzip, Fast-GBS, fasta, FastANI, fastcluster, FastME, FastML, fastp, fastq_pair, fastq_species_detector, FastQC, fastsimcoal26, fastStructure, FastTree, FASTX, feh, fineRADstructure, fineSTRUCTURE, FIt-SNE, flash, flash2, flexbar, Flexible Adapter Remover, Flye, FMAP, FragGeneScan, FragGeneScan, freebayes, FunGene Pipeline, GAEMR, Galaxy, GATK, gatk4, Gblocks, GBRS, gcc, GCTA, GDAL, gdc-client, GEM library, GEMMA, geneid, GeneMark, GeneMarker, Genome STRiP, GenomeMapper, GenomeStudio (Illumina), GenomicConsensus, gensim, GEOS, germline, gerp++, gffread, giggle, GMAP/GSNAP, GNU Compilers, GNU parallel, go-perl, GoShifter, gradle-4.4, graftM, graphviz, GRiD, Grinder, GROMACS, GSEA, GTDB-Tk, GTFtools, Gubbins, GUPPY, HapCompass, HAPCUT, HAPCUT2, hapflk, HaploMerger, Haplomerger2, HapSeq2, HarvestTools, HiC-Pro, HiCExplorer, HISAT2, HMMER, Homer, HOTSPOT, HTSeq, HUMAnN2, hyperopt, HyPhy, iAssembler, IBDLD, IDBA-UD, IDP-denovo, idr, IgBLAST, IGoR, IGV, IMa2, IMa2p, IMAGE, ImageJ, ImageMagick, Immcantation, impute2, IMSA-A, INDELseek, infernal, Infomap, InStruct, InteMAP, InterProScan, ipyrad, IQ-TREE, iRep, jags, java, jbrowse, jellyfish, JoinMap, julia, jupyter, kallisto, Kent Utilities, keras, khmer, KmerFinder, kraken, kSNP, kWIP, LACHESIS, lammps, LAST, lcMLkin, LDAK, leeHom, Lep-MAP3, Lighter, LINKS, LocARNA, LocusZoom, longranger, LUCY, LUCY2, LUMPY, lyve-SET, MACE, MACS, MaCS simulator, MACS2, MAFFT, mafTools, Magic-BLAST, magick, MAKER, MAQ, MASH, mashtree, Mashtree, MaSuRCA, Mauve, MaxBin, mccortex, mcl, megahit, MeGAMerge, MEGAN, MELT, MEME Suite, MERLIN, MetaBAT, MetaCRAST, metaCRISPR, MetAMOS, MetaPathways, MetaPhlAn, MetaVelvet, MetaVelvet-SL, MGmapper, Migrate-n, mikado, Minimac4, minimap2, mira, miRDeep2, MISO (misopy), MITObim, MiXCR, MixMapper, MKTest, mlst, MMAP, MMSEQ, monocle3, mosdepth, mothur, MrBayes, mrsFAST, msld, MSMC, msprime, MSR-CA Genome Assembler, msstats, MSTMap, mugsy, MultiQC, multiz-tba, MUMmer, muscle, MUSIC, muTect, Nanopolish, ncftp, Nemo, Netbeans, NEURON, new_fugue, Nextflow, NextGenMap, nf-core/rnaseq, NGS_data_processing, NGSadmix, ngsDist, ngsF, ngsLD, NgsRelate, ngsTools, NGSUtils, NLR-Parser, Novoalign, NovoalignCS, nvidia-docker, Oases, OBITools, OMA, OrthoFinder, Orthomcl, PacBioTestData, PAGIT, paleomix, PAML, pandas, pandaseq, PanPhlAn, Panseq, Parsnp, PASA, PASTEC, PAUP*, pb-assembly, pbalign, pbh5tools, PBJelly, PBSuite, PCAngsd, PeakRanger, PeakSplitter, PEAR, PEER, PennCNV, PfamScan, PGDSpider, ph5tools, Phage_Finder, PHAST, phenopath, Phobius, PHRAPL, PHYLIP, PhyloCSF, phyloFlash, phylophlan, PhyML, Picard, pigz, Pilon, Pindel, piPipes, PIQ, PlasFlow, Platypus, plink, plink2, Plotly, popbam, PopCOGenT, Porechop, portcullis, pplacer, PRANK, prinseq, prodigal, progenomics, progressiveCactus, PROJ, prokka, psutil, pyani, PyCogent, pyfaidx, pyGenomeTracks, PyMC, pyopencl, pypy, pyRAD, Pyro4, PySnpTools, python, PyTorch, PyVCF, QIIME, QIIME2 q2cli, QTCAT, Quake, Qualimap, QuantiSNP2, QUAST, QUMA, R, RACA, racon, RADIS, RadSex, RAPTR-SV, RAxML, Ray, Rcorrector, RDP Classifier, REAPR, Relate, RelocaTE2, RepeatMasker, RepeatModeler, RFMix, rgdal, RGI, Rgtsvm, ripgrep, rJava, RNAMMER, rnaQUAST, Rnightlights, Roary, Rqtl, Rqtl2, RSEM, RSeQC, RStudio, rtfbs_db, sabre, SaguaroGW, salmon, Sambamba, samblaster, SampleTracker, Samtools, Satsuma, Satsuma2, scikit-learn, Scoary, scythe, seaborn, SecretomeP, selscan, Sentieon, SeqPrep, seqtk, Seurat, sf, sgrep, sgrep sorted_grep, SHAPEIT, shore, SHOREmap, shortBRED, SHRiMP, sickle, SignalP, simuPOP, singularity, sistr_cmd, SKESA, skewer, SLiM, smcpp, SMRT Analysis, SMRT LINK, snakemake, snap, SNAPP, snATAC, SNeP, snippy, snp-sites, SnpEff, SNPgenie, SNPhylo, SNVPhyl, SOAP2, SOAPdenovo, SOAPdenovo-Trans, SOAPdenovo2, SomaticSniper, sorted_grep, SPAdes, SparCC, SPARTA, SRA Toolkit, srst2, stacks, Stacks 2, stairway-plot, stampy, STAR, Starcode, statmodels, STITCH, STPGA, StrainPhlAn, strawberry, Strelka, stringMLST, StringTie, STRUCTURE, Structure_threader, supernova, SURPI, sutta, SVDetect, svtools, SWAMP, SweepFinder, sweepsims, tabix, Tandem Repeats Finder (TRF), TargetP, TASSEL 3, TASSEL 4, TASSEL 5, tcoffee, TensorFlow, TEToolkit, tfTarget, TMHMM, tmux, TopHat, Torch, traitRate, Trans-Proteomic Pipeline (TPP), TransComb, TransDecoder, TRANSIT, transrate, TRAP, treeCl, treemix, trimmomatic, Trinity, Trinotate, tRNAscan-SE, UCSC Kent utilities, UMAP, UMI-tools, Unicycler, UniRep, unrar, usearch, Variant Effect Predictor, VarScan, vcf2diploid, vcfCooker, vcflib, vcftools, vdjtools, Velvet, vep, VESPA, vg, ViennaRNA, VIP, viral-ngs, virmap, VirSorter, VirusDetect, VirusFinder 2, VizBin, vmatch, vsearch, vt, WASP, wgs-assembler (Celera), Wise2 (Genewise), Xander_assembler, yaha
Details for R (hide)
| Name: | R |
| Version: | 3.5.0 |
| OS: | Linux |
| About: | R is a free software environment for statistical computing and graphics. |
| Added: | 12/14/2011 10:47:08 AM |
| Updated: | 5/22/2018 11:03:33 AM |
| Link: | http://www.r-project.org/ |
| Notes: | There are two separate R installations for each version of R.
- Command: R The default R uses parallel BLAS library (Basic Linear Algebra Subprograms) that we compiled with multithreading option switched on. This reduces computing time for linear algebra calls by a factor of 3 or more. If you experience any problems (e.g. an error message that "cause 'illegal operand'"), or just do not want to use parallel BLAS for any reason, use the next command.
- Command: /programs//R-3.5.0s/bin/R This R installation uses built-in BLAS library.
Preinstalled packages: Biocondutor edgeR DESeq Hmisc mclust and much much more. Existence and version of a package can be checked with the following command: packageVersion("packagename")
New R v3.6.1 version is installed in /programs/R-3.6.1. To run R 3.6.1, use the command "/programs//R-3.6.1/bin/R". Only R base packages are installed in the new version, you will need to install R packages by yourself in your home directory.
The latest version of the program is in your PATH, and can be used directly by typing its name at the prompt:
R [options]
There are 5 previous version(s) available. Any version can be accessed either by typing full path, or by adding it to the PATH and then typing its name at the prompt. NOTE: you need to set PATH only once per login/session.
| version | access | 3.5.0
(latest) | | full path: | /programs/R-3.5.0/bin/R [options] | | add to PATH: | export PATH=/programs/R-3.5.0/bin:$PATH |
| | 3.4.2 | | full path: | /programs/R-3.4.2/bin/R [options] | | add to PATH: | export PATH=/programs/R-3.4.2/bin:$PATH |
| | 3.3.2 | | full path: | /programs/R-3.3.2/bin/R [options] | | add to PATH: | export PATH=/programs/R-3.3.2/bin:$PATH |
| | 3.2.5 | | full path: | /programs/R-3.2.5/bin/R [options] | | add to PATH: | export PATH=/programs/R-3.2.5/bin:$PATH |
| | 3.2.2 | | full path: | /programs/R-3.2.2/bin/R [options] | | add to PATH: | export PATH=/programs/R-3.2.2/bin:$PATH |
| | 3.1.0 | | full path: | /programs/R-3.1.0/bin/R [options] | | add to PATH: | export PATH=/programs/R-3.1.0/bin:$PATH |
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