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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 pypy (hide)

Name:pypy
Version:2.7&3.5
OS:Linux
About:PyPy is a fast, compliant alternative implementation of the Python language
Added:10/24/2018 9:23:09 PM
Updated:
Link:https://pypy.org/
Notes:

PYPY is implemented with Conda.

To use pypy2.7:

export PATH=/programs/Anaconda2/bin:$PATH

source activate pypy2.7

Command: 

pypy

 

To use pypy3.5:

export PATH=/programs/Anaconda2/bin:$PATH

source activate pypy3.5

Command:

pypy3

 

To exit pypy environment:

source deactivate

 

## for extra python modules

You can request by email any python modules for pypy. In your email, please indicate which pypy (2.7 or 3.5). Alternatively, you can install your own pypy through conda, then you can install any python modules by yourself. 

1. setup conda by following part 1 in this instruction: http://cbsu.tc.cornell.edu/lab/doc/LinuxSoftwareInstallationExer.pdf 

2. to setup pypy 2.7: conda create -n pypy2.7 python=2.7  pypy2.7

To set up pypy3.5: conda create -n pypy3.5 python=3.5 pypy3.5.

3. to use your own pypy installation:

export PATH=~/anaconda2/bin:$PATH

source activate pypyx.x

4. To install extra modules, first activate pypy environment as describ: source activate pypy2.7, Then install modules with this command:

pypy -m pip install numpy

 

 

 


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