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BioHPC Cloud:
: User Guide

 


BioHPC Cloud Software

There is 672 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, amplicon.py, 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, bam2fastx, 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, DESMAN, 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, EGAD, EIGENSOFT, EMBOSS, entropy, ephem, epic2, ermineJ, ete3, exabayes, exonerate, eXpress, FALCON, FALCON_unzip, Fast-GBS, fasta, FastANI, fastcluster, FastME, FastML, fastp, FastQ Screen, 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, gatk4amplicon.py, Gblocks, GBRS, gcc, GCTA, GDAL, gdc-client, GEM library, GEMMA, geneid, GeneMark, GeneMarker, Genome STRiP, GenomeMapper, GenomeStudio (Illumina), GenomicConsensus, gensim, GEOS, germline, gerp++, GET_PHYLOMARKERS, GffCompare, 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, lftp, Lighter, LINKS, LocARNA, LocusZoom, lofreq, longranger, LS-GKM, 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, Minimac3, Minimac4, minimap2, mira, miRDeep2, MISO (misopy), MITObim, MiXCR, MixMapper, MKTest, mlst, MMAP, MMSEQ, MMseqs2, 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, PhyloPhlAn2, 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, rclone, 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, sample, 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, SimPhy, simuPOP, singularity, sistr_cmd, SKESA, skewer, SLiM, smcpp, SMRT Analysis, SMRT LINK, snakemake, snap, SNAPP, snATAC, SNeP, snippy, snp-sites, SnpEff, SNPgenie, SNPhylo, SNPsplit, 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, Trim Galore!, 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 RStudio (hide)

Name:RStudio
Version:1.1.463
OS:Linux
About:RStudio is an integrated development environment (IDE) for R
Added:3/1/2016 7:40:28 PM
Updated:2/14/2019 11:28:19 AM
Link:https://www.rstudio.com/
Manual:https://support.rstudio.com/hc/en-us/categories/200035113-Documentation
Download:https://www.rstudio.com/products/rstudio/download/
Notes:

Both "RStudio Server" and "RStudio Desktop" are implemented on BioHPC. We recommed to run RStudio through "RStudio Server" to get better graphics. The free version of RStudio server runs through http not https, but as BioHPC is only accessible through Cornell local network, it is reasonably safe.

Here are the instructions:

A. Run RStudio Server (recommended)

  1. SSH Login (through Putty or Mac Terminal) to the BioHPC server you want to run RStudio. Make sure that you DO NOT reserve a machine with the tag "enhanced security" on the BioHPC reservation page.
  2. Run the command "/programs/rstudio_server/rstudio_start" to start RStudio server. 
  3. From a brower on your laptop/desktop computer, go to this site "http://cbsuxxxxxx.biohpc.cornell.edu:8015".   (replacing the "cbsuxxxxx" with the acutal machine name ). Sometimes, you might need to reshresh the page once. 
  4. If you want to stop the RStudio Server, using this command "/programs/rstudio_server/rstudio_stop". 

B. Run RStudio Desktop (alternative way)

It is an X-windows software. If you do not know how to run an X-windows software on BioHPC lab, read this page: https://cbsu.tc.cornell.edu/lab/userguide.aspx?a=access#b (read the section under under How to run graphical applications)

To start the software, use this command: /programs/rstudio/bin/rstudio

 


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