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BioHPC Cloud:
: User Guide

 


BioHPC Cloud Software

There is 770 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, AMRFinder, analysis, ANGSD, Annovar, antiSMASH, anvio, apollo, arcs, 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, BarNone, 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, BRAKER, BRAT-NextGen, BreedingSchemeLanguage, breseq, brocc, BSseeker2, BUSCO, BWA, bwa-meth, cactus, CAFE, canu, CAP3, CarveMe, cBar, CBSU RNAseq, CCTpack, cd-hit, cdbfasta, CEGMA, CellRanger, cellranger-atac, cellranger-dna, centrifuge, centroFlye, CFM-ID, CFSAN SNP pipeline, CheckM, chimera, chromosomer, Circlator, Circos, Circuitscape, CITE-seq-Count, CLUMPP, clust, 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, 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, Dsuite, dTOX, duphold, dynare, ea-utils, ecopcr, ecoPrimers, ectyper, EDGE, edirect, eems, EgaCryptor, EGAD, EIGENSOFT, EMBOSS, Empress, entropy, ephem, epic2, ermineJ, ete3, 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, fastsimcoal26, fastStructure, FastTree, FASTX, feh, FFmpeg, fineRADstructure, fineSTRUCTURE, FIt-SNE, flash, flash2, flexbar, Flexible Adapter Remover, Flye, FMAP, FragGeneScan, FragGeneScan, freebayes, FunGene Pipeline, G-PhoCS, GAEMR, Galaxy, GATK, gatk4, gatk4amplicon.py, Gblocks, GBRS, gcc, GCTA, GDAL, gdc-client, GEM library, GEMMA, geneid, GeneMark, GeneMarker, Genome STRiP, GenomeMapper, GenomeStudio (Illumina), GenomeThreader, genometools, GenomicConsensus, gensim, GEOS, germline, gerp++, GET_PHYLOMARKERS, GffCompare, gffread, giggle, glactools, GlimmerHMM, GMAP/GSNAP, GNU Compilers, GNU parallel, go-perl, GO2MSIG, GoShifter, gradle-4.4, graftM, GraPhlAn, graphviz, GRiD, Grinder, GROMACS, GSEA, gsort, GTDB-Tk, GTFtools, Gubbins, GUPPY, hail, HapCompass, HAPCUT, HAPCUT2, hapflk, HaploMerger, Haplomerger2, HapSeq2, HarvestTools, hdf5, hh-suite, HiC-Pro, HiCExplorer, HISAT2, HMMER, Homer, HOTSPOT, HTSeq, htslib, 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, 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, kraken, kSNP, kWIP, LACHESIS, lammps, LAST, lcMLkin, LDAK, leeHom, Lep-MAP3, lftp, Lighter, LinkedSV, LINKS, LocARNA, LocusZoom, lofreq, longranger, LS-GKM, LTR_retriever, LUCY, LUCY2, LUMPY, lyve-SET, MACE, MACS, MaCS simulator, MACS2, MAFFT, mafTools, Magic-BLAST, magick, MAKER, MAQ, MASH, mashtree, Mashtree, MaSuRCA, Mauve, MaxBin, McClintock, mccortex, mcl, MCscan, megahit, MeGAMerge, MEGAN, MELT, MEME Suite, MERLIN, MetaBAT, MetaCRAST, metaCRISPR, MetAMOS, MetaPathways, MetaPhlAn, MetaVelvet, MetaVelvet-SL, MGmapper, Migrate-n, mikado, MinCED, Minimac3, Minimac4, minimap2, mira, miRDeep2, MISO (misopy), MITObim, MiXCR, MixMapper, MKTest, mlst, MMAP, MMSEQ, MMseqs2, moments, mono, monocle3, mosdepth, mothur, MrBayes, mrsFAST, msld, MSMC, msprime, MSR-CA Genome Assembler, msstats, MSTMap, mugsy, MultiQC, multiz-tba, MUMmer, muscle, MUSIC, muTect, nag-compiler, nanofilt, Nanopolish, ncftp, NECAT, Nemo, Netbeans, NEURON, new_fugue, Nextflow, NextGenMap, nf-core/rnaseq, NGS_data_processing, NGSadmix, ngsDist, ngsF, ngsLD, NgsRelate, ngsTools, NGSUtils, NINJA, NLR-Annotator, NLR-Parser, Novoalign, NovoalignCS, NRSA, nvidia-docker, Oases, OBITools, Octave, OMA, openmpi, OrthoFinder, orthologr, Orthomcl, pacbio, PacBioTestData, PAGIT, paleomix, PAML, panaroo, pandas, pandaseq, PanPhlAn, Panseq, Parsnp, PASA, PASTEC, PAUP*, pb-assembly, pbalign, pbbam, pbh5tools, PBJelly, pbmm2, PBSuite, PCAngsd, pcre, pcre2, PeakRanger, PeakSplitter, PEAR, PEER, PennCNV, peppro, PfamScan, pgap, PGDSpider, ph5tools, Phage_Finder, PHAST, phenopath, Phobius, PHRAPL, PHYLIP, PhyloCSF, phyloFlash, phylophlan, PhyloPhlAn2, phylophlan3, PhyML, Picard, pigz, Pilon, Pindel, piPipes, PIQ, PlasFlow, Platypus, plink, plink2, Plotly, popbam, PopCOGenT, Porechop, portcullis, pplacer, PRANK, prinseq, prodigal, progenomics, progressiveCactus, PROJ, prokka, Proseq2, PSASS, psutil, pyani, PyCogent, pycoQC, pyfaidx, pyGenomeTracks, PyMC, pyopencl, pypy, pyRAD, Pyro4, PySnpTools, python, PyTorch, PyVCF, QIIME, QIIME2, QTCAT, Quake, Qualimap, QuantiSNP2, QUAST, QUMA, R, RACA, racon, RADIS, RadSex, RAPTR-SV, RAxML, raxml-ng, Ray, rclone, Rcorrector, RDP Classifier, REAGO, REAPR, ReferenceSeeker, Relate, RelocaTE2, RepeatMasker, RepeatModeler, RERconverge, RFMix, rgdal, RGI, Rgtsvm, ripgrep, rJava, RNAMMER, rnaQUAST, Rnightlights, Roary, Rqtl, Rqtl2, RSEM, RSeQC, RStudio, rtfbs_db, ruby, sabre, SaguaroGW, salmon, Sambamba, samblaster, sample, SampleTracker, samtabix, Samtools, Satsuma, Satsuma2, SCALE, scanorama, scikit-learn, Scoary, scythe, seaborn, SecretomeP, selscan, Sentieon, SeqPrep, seqtk, Seurat, sf, sgrep, sgrep sorted_grep, SHAPEIT, SHAPEIT4, shasta, Shiny, shore, SHOREmap, shortBRED, SHRiMP, sickle, SignalP, SimPhy, simuPOP, singularity, sinto, sistr_cmd, SKESA, skewer, SLiM, SLURM, smcpp, smoove, SMRT Analysis, SMRT LINK, snakemake, snap, SnapATAC, SNAPP, snATAC, SNeP, snippy, snp-sites, SnpEff, SNPgenie, SNPhylo, SNPsplit, SNVPhyl, SOAP2, SOAPdenovo, SOAPdenovo-Trans, SOAPdenovo2, SomaticSniper, sorted_grep, spaceranger, SPAdes, SPALN, SparCC, SPARTA, sqlite, 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, SV-plaudit, SVDetect, SVseq2, svtools, svtyper, SWAMP, SweepFinder, sweepsims, tabix, Taiji, Tandem Repeats Finder (TRF), tardis, TargetP, TASSEL 3, TASSEL 4, TASSEL 5, tbl2asn, tcoffee, TensorFlow, TEToolkit, texlive, tfTarget, 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, unrar, usearch, Variant Effect Predictor, VarScan, VCF-kit, 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 smoove (hide)

Name:smoove
Version:0.2.5
OS:Linux
About:structural variant calling and genotyping with existing tools, but, smoothly.
Added:5/19/2020 10:57:46 AM
Updated:
Link:https://github.com/brentp/smoove
Notes:

## The instructions below are for running smoove through docker

## Prepare data files. Create a workdir, it must be "/workdir/$USER", and copy your data files in this directory.

mkdir /workdir/$USER

##Run command. The first time you run it on the machine, it will take a few minutes to download the docker image to your computer. Next time you run it, the local image will be used.

docker1 run --rm -it brentp/smoove smoove -h

**IMPORTANT**

You should put all your input data files under the directory "/workdir/$USER". This directory is mounted as "/workdir/" within the docker container.  As the command "smoove" is actually run within the Docker container,  you should use the path "/workdir/*" for your input files.  The same thing goes for the output directory.  You should specify "/workdir/results-smoove/" in the command, and you will see the results in "/workdir/$USER/results-smoove". For example, your command should be like  (change -p to the number of CPU core of your computer):

docker1 run --rm -it brentp/smoove sh -c 'smoove call -x --name my-cohort --exclude /workdir/my.bed --fasta /workdir/my.fasta -p 24 --genotype /workdir/*.bam --outdir /workdir/results-smoove'

After job is finished, you should get the results under /workdir/$USER/results-smoove/.

The output directory is owned by root. Run this command to change ownership back to you.

docker1 claim

If you are not going to use the software for a while, you need to delete the docker image on the local computer

docker1 images
docker1 rmi brentp/smoove

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