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BioHPC Cloud:
: User Guide

 


BioHPC Cloud Software

There is 569 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, Admixtools, Admixture, agrep, albacore, Alder, AlleleSeq, ALLMAPS, ALLPATHS-LG, AMOS, AMPHORA, analysis, ANGSD, Annovar, antiSMASH, apollo, Arlequin, aspera, atac-seq-pipeline, Atlas-Link, ATLAS_GapFill, ATSAS, Augustus, AWS command line interface, axe, bamtools, Basset, BayeScan, Bayescenv, BBmap, BCFtools, bcl2fastq, BCP, Beagle, Beagle4, Beast2, bedops, BEDtools, bfc, bgc, bgen, bigQF, bigWig, bioawk, biobambam, Bioconductor, biom-format, BioPerl, BioPython, Birdsuite, Bismark, blasr, BLAST, blast2go, BLAT, BMGE, bmtagger, Boost, Bowtie, Bowtie2, BPGA, BreedingSchemeLanguage, breseq, BSseeker2, BUSCO, BWA, bwa-meth, cactus, canu, CAP3, cBar, CBSU RNAseq, CCTpack, cd-hit, CEGMA, CellRanger, centrifuge, CFSAN SNP pipeline, CheckM, 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, dDocent, DeconSeq, deepTools, defusion, delly, destruct, DETONATE, diamond, diploSHIC, Discovar, Discovar de novo, distruct, DIYABC, Docker, dREG, dREG.HD, Drop-seq, dropSeqPipe, dsk, ea-utils, ecopcr, ectyper, EDGE, edirect, eems, EIGENSOFT, EMBOSS, entropy, ephem, ermineJ, ete3, exabayes, exonerate, eXpress, FALCON, FALCON_unzip, Fast-GBS, fasta, fastcluster, FastML, fastp, fastq_species_detector, FastQC, fastsimcoal26, fastStructure, FastTree, FASTX, fineRADstructure, fineSTRUCTURE, FIt-SNE, flash, flash2, flexbar, Flexible Adapter Remover, Flye, FMAP, FragGeneScan, freebayes, FunGene Pipeline, GAEMR, Galaxy, GATK, gatk4, GBRS, gcc, GCTA, gdc-client, GEM library, GEMMA, geneid, GeneMark, GeneMarker, Genome STRiP, GenomeMapper, GenomeStudio (Illumina), GenomicConsensus, gensim, germline, gffread, giggle, GMAP/GSNAP, GNU Compilers, GNU parallel, gradle-4.4, graftM, graphviz, Grinder, GROMACS, GSEA, GTFtools, Gubbins, 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, IgBLAST, IGoR, IGV, IMa2, IMa2p, IMAGE, ImageJ, impute2, IMSA-A, INDELseek, infernal, InStruct, InteMAP, InterProScan, ipyrad, IQ-TREE, iRep, jags, java, jbrowse, jellyfish, JoinMap, julia, jupyter, kallisto, Kent Utilities, keras, khmer, KmerFinder, kraken, kSNP, kWIP, LACHESIS, LAST, lcMLkin, LDAK, leeHom, Lep-MAP3, Lighter, LINKS, LocusZoom, longranger, LUCY, LUCY2, LUMPY, lyve-SET, MACS, MaCS simulator, MACS2, MAFFT, mafTools, Magic-BLAST, MAKER, MAQ, MASH, MaSuRCA, Mauve, MaxBin, mccortex, mcl, megahit, MeGAMerge, MEGAN, MELT, MEME Suite, MERLIN, MetaBAT, metaCRISPR, MetAMOS, MetaPathways, MetaPhlAn, MetaVelvet, MetaVelvet-SL, MGmapper, Migrate-n, mikado, Minimac4, mira, miRDeep2, MISO (misopy), MITObim, MixMapper, MKTest, MMAP, MMSEQ, mosdepth, mothur, MrBayes, mrsFAST, msld, MSMC, msprime, MSR-CA Genome Assembler, msstats, MSTMap, mugsy, MultiQC, MUMmer, muscle, MUSIC, muTect, Nanopolish, ncftp, Nemo, Netbeans, NEURON, new_fugue, NextGenMap, NGS_data_processing, NGSadmix, ngsDist, ngsF, ngsTools, NGSUtils, NLR-Parser, Novoalign, NovoalignCS, nvidia-docker, Oases, OBITools, Orthomcl, PacBioTestData, PAGIT, paleomix, PAML, pandas, pandaseq, PanPhlAn, Panseq, Parsnp, PASA, PASTEC, PAUP*, pbalign, pbh5tools, PBJelly, PBSuite, PeakRanger, PeakSplitter, PEAR, PEER, PennCNV, PfamScan, PGDSpider, ph5tools, Phage_Finder, PHAST, PHRAPL, PHYLIP, PhyloCSF, phylophlan, PhyML, Picard, pigz, Pilon, Pindel, piPipes, PIQ, PlasFlow, Platypus, plink, plink2, Plotly, popbam, Porechop, portcullis, prinseq, prodigal, progressiveCactus, prokka, psutil, pyani, PyCogent, pyfaidx, pyGenomeTracks, PyMC, 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, RepeatMasker, RepeatModeler, RFMix, RGI, Rgtsvm, ripgrep, RNAMMER, rnaQUAST, Roary, Rqtl, Rqtl2, RSEM, RSeQC, RStudio, rtfbs_db, sabre, SaguaroGW, salmon, Sambamba, samblaster, SampleTracker, Samtools, Satsuma, Satsuma2, scikit-learn, Scoary, scythe, seaborn, selscan, Sentieon, SeqPrep, seqtk, Seurat, 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, SNPhylo, 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, strawberry, Strelka, stringMLST, StringTie, STRUCTURE, supernova, SURPI, sutta, SVDetect, svtools, SweepFinder, sweepsims, tabix, Tandem Repeats Finder (TRF), TASSEL 3, TASSEL 4, TASSEL 5, tcoffee, TensorFlow, TEToolkit, TMHMM, tmux, TopHat, Torch, traitRate, Trans-Proteomic Pipeline (TPP), TransComb, TransDecoder, transrate, TRAP, treeCl, treemix, trimmomatic, Trinity, Trinotate, tRNAscan-SE, UCSC Kent utilities, UMAP, UMI-tools, Unicycler, unrar, usearch, Variant Effect Predictor, VarScan, vcf2diploid, vcfCooker, vcflib, vcftools, vdjtools, Velvet, vep, VESPA, vg, ViennaRNA, VIP, VirSorter, VirusDetect, VirusFinder 2, VizBin, vmatch, vsearch, WASP, wgs-assembler (Celera), Wise2 (Genewise), Xander_assembler, yaha

Details for BPGA (hide)

Name:BPGA
Version:1.3
OS:Linux
About:Comprehensive pan genome analysis of microorganisms
Added:10/25/2017 2:11:29 PM
Updated:
Link:http://www.iicb.res.in/bpga/index.html
Manual:https://sourceforge.net/projects/bpgatool/files/BPGA%20User%20Manual.pdf
Download:https://sourceforge.net/projects/bpgatool/files/
Notes:

The pipeline is implemented as a docker image. (Check https://cbsu.tc.cornell.edu/lab/userguide.aspx?a=software&i=340#c for more information about docker)

 

1. Prepare data files (replace yyyyy with your User ID) 

### create a working directory

mkdir /workdir/yyyyy

### then put your data files in the working directory

 

2. Load the docker image:

docker1 import /programs/BPGA-1.3/BPGA-1.3.tar

 

3. Start docker container

## get the image ID

docker1 images

## start docker container (replace xxxxxx in the container with the Image ID from previous command)

docker1 run -d -it xxxxxx  /bin/bash 

 

4. Connect to docker container

## get the Container ID

docker1 ps -a

## connect to the container (replace zzzzz with the container ID from last command)

docker1 exec -it zzzzzzz /bin/bash 

 

5. Now you are in docker, in which you have root privilege. All data files in /workdir/yyyyy of the host machine now are in /workdir inside docker.

 

6. Run BPGA.

cd /usr/local/BPGA-Version-1.3/bin

./BPGA-Version-1.3

 

7. After you are done, put the output files in /workdir.

 

8. You can exist Docker at anytime and reconnect by command "docker1 exec -it zzzzzzz /bin/bash"

 

 

 


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