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BioHPC Cloud:
: User Guide

 


BioHPC Cloud Software

There is 928 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, 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, 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, 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, compat, CONCOCT, Conda, Cooler, copyNumberDiff, cortex_var, CoverM, CRISPRCasFinder, CRISPResso, CrossMap, CRT, cuda, Cufflinks, cutadapt, cuteSV, 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, drive, Drop-seq, dropEst, dropSeqPipe, dsk, dssat, Dsuite, dTOX, duphold, dynare, ea-utils, ecopcr, ecoPrimers, ectyper, EDGE, edirect, EDTA, eems, EgaCryptor, EGAD, EIGENSOFT, elai, 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, 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, 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, HapSeq2, HarvestTools, haslr, hdf5, hget, hh-suite, HiC-Pro, HiCExplorer, 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, LAST, lastz, lcMLkin, LDAK, LeafCutter, leeHom, lep-anchor, Lep-MAP3, lftp, Liftoff, Lighter, LinkedSV, LINKS, 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, mapDamage, MAQ, MARS, MASH, mashtree, Mashtree, MaSuRCA, MATLAB, Matlab_runtime, Mauve, MaxBin, MaxQuant, McClintock, mccortex, mcl, MCscan, MCScanX, medusa, megahit, MeGAMerge, MEGAN, MELT, MEME Suite, MERLIN, MetaBAT, MetaCache, MetaCRAST, metaCRISPR, MetAMOS, MetaPathways, MetaPhlAn, metaron, MetaVelvet, MetaVelvet-SL, methpipe, mfeprimer, MGmapper, Migrate-n, mikado, MinCED, Minimac3, Minimac4, minimap2, mira, miRDeep2, MISO (misopy), MITObim, 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, 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, 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, PfamScan, pgap, PGDSpider, ph5tools, Phage_Finder, 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, 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, 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, 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, supernova, SURPI, sutta, SV-plaudit, SVDetect, SVseq2, svtools, svtyper, SWAMP, sweed, SweepFinder, SweepFinder2, sweepsims, tabix, 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, wget, wgs-assembler (Celera), windowmasker, Wise2 (Genewise), wombat, Xander_assembler, xpclr, yaha

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

Name:apollo
Version:20170925
OS:Linux
About:Manual genome annotation
Added:9/25/2017 11:12:33 PM
Updated:
Link:https://github.com/GMOD/docker-apollo
Notes:

1. Set up jbrowse directory, following instructions on https://biohpc.cornell.edu/lab/userguide.aspx?a=software&i=357#c

2. Import Docker image:

docker1 pull gmod/apollo

3. Data directories.

After you setup jbrowse, you should have a genome directory, e.g. /workdir/$USER/jbrowse_data

Apollo also needs an extra postgres database directory. This directory must be under /workdir/$USER, and read/write/executable by everyone.

mkdir -p /workdir/$USER/pg_data

chmod a+rwX /workdir/$USER/pg_data

4. Start docker container. It will take  a few minutes for the web server is ready

docker1 run -dit  -v /workdir/$USER/jbrowse_data/:/data -v /workdir/$USER/pg_data:/var/lib/postgresql -p 8031:8080 gmod/apollo

5. Open a web browser (use vpn if you are off campus),open page: http://cbsuxxxxx.biohpc.cornell.edu:8031

The default user name and password is "admin@local.host" "password". You can change the password after you login for the first time. 

6. Click "Organism" tab, and click "Add new organism". Fill out the first 4 fields (The "Directroy" field should be "/data"). Click "Create organism".


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