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BioHPC Cloud:
: User Guide

 


BioHPC Cloud Software

There is 959 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-dna, 454 gsAssembler or gsMapper, a5, ABRicate, ABruijn, ABySS, AdapterRemoval, adephylo, Admixtools, Admixture, agrep, albacore, Alder, AliTV-Perl interface, AlleleSeq, ALLMAPS, ALLPATHS-LG, Alphafold, AMOS, AMPHORA, amplicon.py, AMRFinder, analysis, ANGSD, Annovar, ant, antiSMASH, anvio, apollo, arcs, ARGweaver, Arlequin, ART, 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, BactSNP, bakta, bam2fastx, bamsurgeon, bamtools, bamUtil, barcode_splitter, BarNone, Basset, BayeScan, Bayescenv, baypass, bazel, BBMap/BBTools, BCFtools, bcl2fastq, BCP, Beagle, Beast2, bedops, BEDtools, bfc, bgc, bgen, bigQF, bigWig, bioawk, biobakery, biobambam, Bioconductor, biom-format, BioPerl, BioPython, Birdsuite, 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, BSseeker2, BUSCO, BWA, bwa-mem2, bwa-meth, bwtool, cactus, CAFE, caffe, cagee, canu, CAP3, caper, CarveMe, catch, cBar, CBSU RNAseq, CCMetagen, CCTpack, cd-hit, cdbfasta, CEGMA, CellRanger, cellranger-arc, cellranger-atac, cellranger-dna, centrifuge, centroFlye, CFM-ID, CFSAN SNP pipeline, CheckM, chimera, chip-seq-pipeline, chromosomer, Circlator, Circos, Circuitscape, CITE-seq-Count, ClermonTyping, clues, CLUMPP, clust, Clustal Omega, CLUSTALW, Cluster, cmake, CMSeq, CNVnator, colabfold, compat, CONCOCT, Conda, Cooler, copyNumberDiff, cortex_var, CoverM, CRISPRCasFinder, CRISPResso, CrossMap, CRT, cuda, Cufflinks, cutadapt, cuteSV, dadi, dadi-1.6.3_modif, danpos, DAS_Tool, DBSCAN-SWA, dDocent, DeconSeq, Deepbinner, DeepTE, deepTools, defusion, delly, DESMAN, destruct, DETONATE, diamond, diploSHIC, discoal, Discovar, Discovar de novo, distruct, DiTASiC, DIYABC, Docker, dREG, dREG.HD, drep, Drop-seq, dropEst, dropSeqPipe, dsk, dssat, Dsuite, dTOX, duphold, dynare, ea-utils, ecopcr, ecoPrimers, ectyper, EDGE, edirect, EDTA, eems, EgaCryptor, EGAD, EIGENSOFT, elai, EMBLmyGFF3, EMBOSS, EMIRGE, Empress, entropy, epa-ng, ephem, epic2, ermineJ, ete3, EVM, exabayes, exonerate, ExpansionHunterDenovo-v0.8.0, eXpress, FALCON, FALCON_unzip, Fast-GBS, fasta, FastANI, fastcluster, FastME, FastML, fastp, FastQ Screen, fastq_pair, fastq_species_detector, FastQC, fastqsplitter, fastsimcoal2, fastspar, fastStructure, FastTree, FASTX, feems, feh, FFmpeg, fgbio, Filtlong, fineRADstructure, fineSTRUCTURE, FIt-SNE, flash, flash2, flexbar, Flexible Adapter Remover, Flye, FMAP, FragGeneScan, FragGeneScan, freebayes, FSA, funannotate, FunGene Pipeline, G-PhoCS, GADMA, GAEMR, Galaxy in Docker, Galaxy Server, GATK, gatk4, gatk4amplicon.py, gblastn, Gblocks, GBRS, gcc, GCTA, GDAL, gdc-client, GEM library, GEMMA, GENECONV, geneid, GeneMark, GeneMarker, Genome STRiP, Genome Workbench, GenomeMapper, GenomeStudio (Illumina), GenomeThreader, genometools, GenomicConsensus, genozip, gensim, GEOS, germline, gerp++, GET_PHYLOMARKERS, GffCompare, gffread, giggle, git, glactools, GlimmerHMM, GMAP/GSNAP, GNU Compilers, GNU parallel, go-perl, GO2MSIG, GoShifter, gradle-4.4, graftM, grammy, GraPhlAn, graphtyper, graphviz, GRiD, Grinder, GROMACS, GroopM, GSEA, gsort, GTDB-Tk, GTFtools, Gubbins, GUPPY, hail, HapCompass, HAPCUT, HAPCUT2, hapflk, HaploMerger, Haplomerger2, haplostrips, HaploSync, HapSeq2, HarvestTools, haslr, hdf5, hget, hh-suite, HiC-Pro, HiCExplorer, hifiasm, HISAT2, HMMER, Homer, HOTSPOT, HTSeq, htslib, https://github.com/CVUA-RRW/RRW-PrimerBLAST, humann, HUMAnN2, hyperopt, HyPhy, hyphy-analyses, iAssembler, IBDLD, idba, IDBA-UD, IDP-denovo, idr, idseq, IgBLAST, IGoR, IGV, IMa2, IMa2p, IMAGE, ImageJ, ImageMagick, Immcantation, impute2, IMSA-A, INDELseek, infernal, Infomap, inStrain, InStruct, Intel MKL, InteMAP, InterProScan, ipyrad, IQ-TREE, iRep, jags, Jane, java, jbrowse, JCVI, jellyfish, JoinMap, juicer, julia, jupyter, kallisto, Kent Utilities, keras, khmer, kinfin, king, KmerFinder, KmerGenie, kraken, KrakenTools, KronaTools, kSNP, kWIP, LACHESIS, lammps, LAPACK, LAST, lastz, lcMLkin, LDAK, LeafCutter, leeHom, lep-anchor, Lep-MAP3, lftp, Liftoff, Lighter, LinkedSV, LINKS, localcolabfold, LocARNA, LocusZoom, lofreq, longranger, LS-GKM, LTR_retriever, LUCY, LUCY2, LUMPY, lyve-SET, MACE, MACS, MaCS simulator, MACS2, maffilter, MAFFT, mafTools, MAGeCK, MAGeCK-VISPR, Magic-BLAST, magick, MAKER, manta, mapDamage, 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, MetaCache, MetaCRAST, metaCRISPR, MetAMOS, MetaPathways, MetaPhlAn, metapop, metaron, MetaVelvet, MetaVelvet-SL, methpipe, mfeprimer, MGmapper, Migrate-n, mikado, MinCED, Minimac3, Minimac4, minimap2, mira, miRDeep2, mirge3, miRquant, MISO (misopy), MITObim, mitohelper, MiXCR, MixMapper, MKTest, mlift, mlst, MMAP, MMSEQ, MMseqs2, MMTK, modeltest, MODIStsp-2.0.5, module, moments, mono, monocle3, mosdepth, mothur, MrBayes, mrsFAST, msld, MSMC, msprime, MSR-CA Genome Assembler, msstats, MSTMap, mugsy, MultiQC, multiz-tba, MUMandCo, MUMmer, mummer2circos, muscle, MUSIC, Mutation-Simulator, muTect, MZmine, nag-compiler, nanofilt, NanoPlot, Nanopolish, nanovar, ncftp, ncl, NECAT, Nemo, Netbeans, NEURON, new_fugue, Nextflow, NextGenMap, nf-core/rnaseq, ngmlr, NGS_data_processing, NGSadmix, ngsDist, ngsF, ngsLD, NgsRelate, ngsTools, NGSUtils, NINJA, NLR-Annotator, NLR-Parser, Novoalign, NovoalignCS, nQuire, NRSA, NuDup, numactl, nvidia-docker, nvtop, Oases, OBITools, Octave, OMA, Oneflux, OpenBLAS, openmpi, openssl, OrthoFinder, orthologr, Orthomcl, pacbio, PacBioTestData, PAGIT, pal2nal, paleomix, PAML, panaroo, pandas, pandaseq, pandoc, PanPhlAn, Panseq, Parsnp, PASA, PASTEC, PAUP*, pb-assembly, pbalign, pbbam, pbh5tools, PBJelly, pblat, pbmm2, PBSuite, pbsv, PCAngsd, pcre, pcre2, PeakRanger, PeakSplitter, PEAR, PEER, PennCNV, peppro, PERL, PfamScan, pgap, PGDSpider, ph5tools, Phage_Finder, phasedibd, PHAST, phenopath, Phobius, PHRAPL, PHYLIP, PhyloCSF, phyloFlash, phylophlan, PhyloPhlAn2, phylophlan3, PhyML, Picard, PICRUSt2, pigz, Pilon, Pindel, piPipes, PIQ, PlasFlow, platanus, Platypus, plink, plink2, Plotly, Point Cloud Library, popbam, PopCOGenT, PopLDdecay, Porechop, poretools, portcullis, POUTINE, pplacer, PRANK, preseq, primalscheme, primer3, PrimerBLAST, PrimerPooler, prinseq, prodigal, progenomics, progressiveCactus, PROJ, prokka, Proseq2, ProtExcluder, protolite, PSASS, psmc, psutil, purge_dups, pyani, PyCogent, pycoQC, pyfaidx, pyGenomeTracks, PyMC, pymol-open-source, pyopencl, pypy, pyRAD, Pyro4, pyseer, PySnpTools, python, PyTorch, PyVCF, qcat, QIIME, QIIME2, QTCAT, Quake, Qualimap, QuantiSNP2, QUAST, quickmerge, QUMA, R, RACA, racon, rad_haplotyper, RADIS, RadSex, RagTag, rapt, RAPTR-SV, RATT, RAxML, raxml-ng, Ray, rclone, Rcorrector, RDP Classifier, REAGO, REAPR, Rebaler, Red, ReferenceSeeker, regenie, Relate, RelocaTE2, Repbase, RepeatMasker, RepeatModeler, RERconverge, RFMix, RGAAT, rgdal, RGI, Rgtsvm, Ribotaper, ripgrep, rJava, rMATS, RNAMMER, rnaQUAST, Rnightlights, Roary, Rockhopper, rohan, rphast, Rqtl, Rqtl2, RSEM, RSeQC, RStudio, rtfbs_db, ruby, sabre, SaguaroGW, salmon, Sambamba, samblaster, sample, SampleTracker, samplot, samtabix, Samtools, Satsuma, Satsuma2, SCALE, scanorama, scikit-learn, Scoary, scythe, seaborn, SEACR, SecretomeP, selscan, Sentieon, seqkit, SeqPrep, seqtk, Seurat, sf, sgrep, sgrep sorted_grep, SHAPEIT, SHAPEIT4, shasta, Shiny, shore, SHOREmap, shortBRED, SHRiMP, sickle, sift4g, SignalP, SimPhy, simuPOP, singularity, sinto, sistr_cmd, SKESA, skewer, SLiM, SLURM, smcpp, smoove, SMRT Analysis, SMRT LINK, snakemake, snap, SnapATAC, SNAPP, snATAC, SNeP, Sniffles, snippy, snp-sites, SnpEff, SNPgenie, SNPhylo, SNPsplit, SNVPhyl, SOAP2, SOAPdenovo, SOAPdenovo-Trans, SOAPdenovo2, SomaticSniper, sorted_grep, spaceranger, SPAdes, SPALN, SparCC, SPARTA, split-fasta, sqlite, SRA Toolkit, srst2, stacks, Stacks 2, stairway-plot, stampy, STAR, Starcode, statmodels, STITCH, STPGA, StrainPhlAn, strawberry, Strelka, stringMLST, StringTie, STRUCTURE, Structure_threader, Struo2, stylegan2-ada-pytorch, subread, sumatra, supernova, SURPI, surpyvor, sutta, SV-plaudit, SVDetect, SVseq2, svtools, svtyper, SWAMP, sweed, SweepFinder, SweepFinder2, sweepsims, tabix, tagdust, Taiji, Tandem Repeats Finder (TRF), tardis, TargetP, TASSEL 3, TASSEL 4, TASSEL 5, tbl2asn, tcoffee, TensorFlow, TEToolkit, TEtranscripts, texlive, TFEA, tfTarget, thermonucleotideBLAST, ThermoRawFileParser, TMHMM, tmux, Tomahawk, TopHat, Torch, traitRate, Trans-Proteomic Pipeline (TPP), TransComb, TransDecoder, TRANSIT, transrate, TRAP, treeCl, treemix, Trim Galore!, trimal, trimmomatic, Trinity, Trinotate, tRNAscan-SE, UCSC Kent utilities, UMAP, UMI-tools, Unicycler, UniRep, unitig-caller, unrar, usearch, vamb, Variant Effect Predictor, VarScan, VCF-kit, vcf2diploid, vcfCooker, vcflib, vcftools, vdjtools, Velvet, vep, VESPA, vg, ViennaRNA, VIP, viral-ngs, virmap, VirSorter, VirusDetect, VirusFinder 2, vispr, VizBin, vmatch, vsearch, vt, WASP, webin-cli, wget, wgs-assembler (Celera), windowmasker, Wise2 (Genewise), wombat, Xander_assembler, xpclr, yaha

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

Name:git
Version:2.35.0
OS:Linux
About:revision control system
Added:1/28/2022 3:13:45 PM
Updated:
Link:https://github.com/git/git
Notes:You need to use full path to the binaries:

/programs/git/bin/git [options]

You can also add the program to your PATH:

export PATH=/programs/git/bin:$PATH

and then use it directly by typing program name at the prompt.

Setting up SSH keys to push to github

From a BioHPC machine, if you do not already have a file ~/.ssh/id_rsa.pub, then use the command:
ssh-keygen -t rsa, and press enter a few times through the questions.

Now there should be a file ~/.ssh/id_rsa.pub. Open this file with your favorite text editor, and copy the entire contents to your clipboard.
 
Now, go to https://github.com/settings/keys
You can add a new SSH key with type 'Authentication Key' and paste the contents of your ~/.ssh/id_rsa.pub file into the Key textbox. The last field of this key will look like an email address. Edit it so that this is the email address associated with your github account. Then click 'Add SSH Key'.
 
You can test if it works so far with the command ssh -T git@github.com from a BioHPC terminal. It should return something like:
X11 forwarding request failed on channel 0
Hi username! You've successfully authenticated, but GitHub does not provide shell access.
 
If that works, then navigate to the directory with your git repository in a BioHPC terminal. If you type the command: git remote -v you should see the repositories you can pull/push from. If you want the 'origin' repository to be github, then use this command to authenticate using the key you just set up:
git remote set-url origin git@github.com:username/repository.git
 
Or, you can add a new remote URL (named 'github' in this example) with a command like:
git remote add github git@github.com:username/repository.git
 
In either of these commands, change username/repository to your github username and repository name. Leave git@github.com as is. After that, you should be able to push to 'origin' or 'github' (depending on which of the above commands you used) without a password or 2FA.
 


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