BioHPC Cloud Software
There is 722 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, analysis, ANGSD, Annovar, antiSMASH, apollo, 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, centrifuge, CFM-ID, CFSAN SNP pipeline, CheckM, chimera, chromosomer, Circlator, Circos, Circuitscape, 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, 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, ea-utils, ecopcr, ecoPrimers, ectyper, EDGE, edirect, eems, EgaCryptor, EGAD, EIGENSOFT, EMBOSS, 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, graphviz, GRiD, Grinder, GROMACS, GSEA, GTDB-Tk, GTFtools, Gubbins, GUPPY, HapCompass, HAPCUT, HAPCUT2, hapflk, HaploMerger, Haplomerger2, HapSeq2, HarvestTools, 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, InteMAP, InterProScan, ipyrad, IQ-TREE, iRep, jags, java, jbrowse, JCVI, jellyfish, JoinMap, juicer, julia, jupyter, kallisto, Kent Utilities, keras, khmer, KmerFinder, kraken, kSNP, kWIP, LACHESIS, lammps, LAST, lcMLkin, LDAK, leeHom, Lep-MAP3, lftp, Lighter, 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, mccortex, mcl, MCscan, megahit, MeGAMerge, MEGAN, MELT, MEME Suite, MERLIN, MetaBAT, MetaCRAST, metaCRISPR, MetAMOS, MetaPathways, MetaPhlAn, MetaVelvet, MetaVelvet-SL, MGmapper, Migrate-n, mikado, Minimac3, Minimac4, minimap2, mira, miRDeep2, MISO (misopy), MITObim, MiXCR, MixMapper, MKTest, mlst, MMAP, MMSEQ, MMseqs2, mono, monocle3, mosdepth, mothur, MrBayes, mrsFAST, msld, MSMC, msprime, MSR-CA Genome Assembler, msstats, MSTMap, mugsy, MultiQC, multiz-tba, MUMmer, muscle, MUSIC, muTect, Nanopolish, ncftp, 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, OMA, OrthoFinder, Orthomcl, pacbio, PacBioTestData, PAGIT, paleomix, PAML, pandas, pandaseq, PanPhlAn, Panseq, Parsnp, PASA, PASTEC, PAUP*, pb-assembly, pbalign, pbbam, pbh5tools, PBJelly, pbmm2, PBSuite, PCAngsd, PeakRanger, PeakSplitter, PEAR, PEER, PennCNV, PfamScan, pgap, PGDSpider, ph5tools, Phage_Finder, PHAST, phenopath, Phobius, PHRAPL, PHYLIP, PhyloCSF, phyloFlash, phylophlan, PhyloPhlAn2, PhyML, Picard, pigz, Pilon, Pindel, piPipes, PIQ, PlasFlow, Platypus, plink, plink2, Plotly, popbam, PopCOGenT, Porechop, portcullis, pplacer, PRANK, prinseq, prodigal, progenomics, progressiveCactus, PROJ, prokka, PSASS, psutil, pyani, PyCogent, pycoQC, pyfaidx, pyGenomeTracks, PyMC, pyopencl, pypy, pyRAD, Pyro4, PySnpTools, python, PyTorch, PyVCF, QIIME, QIIME2 q2cli, 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, 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, Samtools, Satsuma, Satsuma2, scanorama, scikit-learn, Scoary, scythe, seaborn, SecretomeP, selscan, Sentieon, SeqPrep, seqtk, Seurat, sf, sgrep, sgrep sorted_grep, SHAPEIT, shasta, shore, SHOREmap, shortBRED, SHRiMP, sickle, SignalP, SimPhy, simuPOP, singularity, sistr_cmd, SKESA, skewer, SLiM, SLURM, smcpp, 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, 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, SVDetect, SVseq2, svtools, SWAMP, SweepFinder, sweepsims, tabix, Tandem Repeats Finder (TRF), TargetP, TASSEL 3, TASSEL 4, TASSEL 5, tbl2asn, tcoffee, TensorFlow, TEToolkit, texlive, tfTarget, ThermoRawFileParser, TMHMM, tmux, 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 python (hide)
| Name: | python |
| Version: | 2.7.5 & 3.6.5 |
| OS: | Linux |
| About: | PYTHON (how to use different versions) |
| Added: | 10/25/2018 9:18:02 AM |
| Updated: | |
| Notes: | To use python 2.7.5 (default python2 of CentOS):
python or python2
pip2
Shebang line for your script: #!/usr/bin/python
To use python 3.6.5 (default python3 on BioHPC):
python3
pip3
Shebang line for your script: #!/usr/bin/python3
To use python 2.7.15 (latest version of python2 as of 10/26/2018)
python2.7.15
pip2.7.15
Shebang line for your script: #!/usr/local/bin/python2.7.15
To use other python versions, please create your own Conda virtual environment:
1. Install Minicond, following direction in this page: https://conda.io/miniconda.html.
2. Set up python virtual environment of a particular python version.
export PATH=/home/xxxxx/miniconda2/bin:$PATH
conda create -n python2.7.15 python=2.7.15
3. Use the following commands to activate a python virtual environment (set PATH only once for each session). Once the virtual environement is activated for the session, the command "python" or "pip" will correspond to the virtual environment python.
export PATH=/home/xxxxx/anaconda2/bin:$PATH
source activate python2.7.15
4. Install other python modules within the active virtual environment, using numpy as an example.
pip install numpy
5. Exit virtual environment
source deactivate
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