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BioHPC Cloud:
: User Guide

 


BioHPC Cloud Software

There is 506 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, 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, bigQF, bigWig, 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, canu, CAP3, cBar, CBSU RNAseq, cd-hit, CEGMA, CellRanger, centrifuge, CFSAN SNP pipeline, CheckM, chromosomer, Circlator, Circos, Circuitscape, CLUMPP, Clustal Omega, CLUSTALW, Cluster, cmake, CNVnator, compat, CONCOCT, copyNumberDiff, cortex_var, CrossMap, CRT, cuda, Cufflinks, cutadapt, dadi, dadi-1.6.3_modif, dDocent, DeconSeq, deepTools, defusion, delly, destruct, DETONATE, diamond, Discovar, Discovar de novo, distruct, Docker, dREG, dREG.HD, Drop-seq, dropSeqPipe, dsk, ea-utils, ecopcr, EDGE, edirect, EIGENSOFT, EMBOSS, entropy, ephem, ermineJ, ete3, exabayes, exonerate, eXpress, FALCON, FALCON_unzip, Fast-GBS, fasta, fastcluster, FastML, fastp, fastq_species_detector, FastQC, fastStructure, FastTree, FASTX, fineRADstructure, fineSTRUCTURE, flash, flash2, Flexible Adapter Remover, 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, giggle, GMAP/GSNAP, GNU Compilers, GNU parallel, gradle-4.4, graftM, Grinder, GROMACS, GSEA, 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, IGV, IMa2, IMa2p, IMAGE, impute2, IMSA-A, INDELseek, infernal, InStruct, InteMAP, InterProScan, ipyrad, IQ-TREE, iRep, java, jbrowse, jellyfish, JoinMap, julia, jupyter, kallisto, Kent Utilities, khmer, kSNP, kWIP, LACHESIS, LAST, lcMLkin, LDAK, leeHom, Lep-MAP3, LINKS, LocusZoom, longranger, LUCY, LUCY2, LUMPY, lyve-SET, MACS, MaCS simulator, MACS2, MAFFT, mafTools, Magic-BLAST, MAKER, MAQ, MASH, MaSuRCA, Mauve, MaxBin, mccortex, megahit, MeGAMerge, MEGAN, MELT, MEME Suite, MERLIN, MetaBAT, metaCRISPR, MetAMOS, MetaPathways, MetaPhlAn, MetaVelvet, MetaVelvet-SL, Migrate-n, mira, miRDeep2, MISO (misopy), MixMapper, MKTest, MMAP, MMSEQ, mothur, MrBayes, mrsFAST, msld, MSMC, msprime, MSR-CA Genome Assembler, msstats, MSTMap, mugsy, MultiQC, MUMmer, muscle, MUSIC, muTect, ncftp, Nemo, Netbeans, NEURON, new_fugue, NextGenMap, NGS_data_processing, NGSadmix, ngsDist, ngsF, ngsTools, NGSUtils, NLR-Parser, Novoalign, NovoalignCS, Oases, OBITools, Orthomcl, PacBioTestData, PAGIT, PAML, pandas, pandaseq, PanPhlAn, Panseq, Parsnp, PASA, PASTEC, PAUP*, pbalign, pbh5tools, PBJelly, PBSuite, PeakRanger, PeakSplitter, PEAR, PennCNV, PfamScan, PGDSpider, ph5tools, Phage_Finder, PHAST, PHRAPL, PHYLIP, PhyloCSF, phylophlan, PhyML, Picard, Pilon, Pindel, piPipes, PIQ, PlasFlow, Platypus, plink, Plotly, popbam, prinseq, prodigal, progressiveCactus, prokka, pyani, pyfaidx, pyGenomeTracks, PyMC, pyRAD, Pyro4, PySnpTools, PyTorch, PyVCF, QIIME, QIIME2 q2cli, QTCAT, Quake, Qualimap, QuantiSNP2, QUAST, QUMA, R, RACA, racon, RADIS, RAPTR-SV, RAxML, Ray, Rcorrector, RDP Classifier, REAPR, RepeatMasker, RepeatModeler, RFMix, RGI, RNAMMER, rnaQUAST, Roary, Rqtl, Rqtl2, RSEM, RSeQC, RStudio, rtfbs_db, sabre, SaguaroGW, salmon, Sambamba, samblaster, SampleTracker, Samtools, Satsuma, Satsuma2, scikit-learn, Scoary, scythe, selscan, Sentieon, SeqPrep, seqtk, sgrep, sgrep sorted_grep, SHAPEIT, shore, SHOREmap, shortBRED, SHRiMP, sickle, SignalP, simuPOP, sistr_cmd, skewer, SLiM, smcpp, SMRT Analysis, SMRT LINK, snakemake, snap, SNAPP, snATAC, SNeP, snippy, SNPhylo, SOAP2, SOAPdenovo, SOAPdenovo-Trans, SOAPdenovo2, SomaticSniper, sorted_grep, SPAdes, SparCC, SRA Toolkit, srst2, stacks, Stacks 2, stampy, STAR, statmodels, STITCH, STPGA, 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, traitRate, Trans-Proteomic Pipeline (TPP), TransComb, TransDecoder, transrate, TRAP, treeCl, treemix, trimmomatic, Trinity, Trinotate, tRNAscan-SE, UCSC Kent utilities, UMI-tools, Unicycler, unrar, usearch, Variant Effect Predictor, VarScan, vcf2diploid, vcfCooker, vcflib, vcftools, Velvet, VESPA, ViennaRNA, VIP, VirSorter, VirusDetect, VirusFinder 2, VizBin, vsearch, WASP, wgs-assembler (Celera), Wise2 (Genewise), Xander_assembler, yaha

Details for stacks (hide)

Name:stacks
Version:1.48
OS:Linux
About:Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
Added:12/13/2011 3:19:39 PM
Updated:1/3/2018 7:48:32 PM
Link:http://creskolab.uoregon.edu/stacks/
Platform:Ilumina
Notes:

To run Stacks v2, please use instruction in this page:

https://cbsu.tc.cornell.edu/lab/userguide.aspx?a=software&i=454#c

 

### replace xxxxxxx with docker container ID you get from the previous step

Step1. Run pipeline without web tools 

Stacks executables are located in the directory /programs/stacks/bin, accessible on all BioHPC Lab machines.To launch these executables, please use the full path, e.g.,

/programs/stacks/bin/ref_map.pl [options]

/programs/stacks/bin/denovo_map.pl [options]

/programs/stacks/bin/rxstacks [options]

Parts of stacks which do not need access to the MySQL database or apache web server, such as scripts ref_map.pl and denovo_map.pl executed with the "-S" option, can be run on any machine with memory sufficuent for your problem.

 

Step2. Run pipeline without web tools 

If you need to use mysql and web access, we have switched to a docker implementation which can be implemented on any machine. Please follow this procedure. (replace MyUserID with your BioHPC ID)

1. Prepare working directory. 

mkdir /workdir/MyUserID

cd /workdir/MyUserID

cp -r /programs/stacks/mysql ./

mkdir export

chmod -R uog+rw export

chmod -R uog+rw mysql

 

2. Start docker

docker1 import /programs/stacks/stacks.tar

docker1  run -p 8009:8 -d -it biohpc_MyUserID/stacks start.sh

 

 

3. Prepare SQL database in docker

## run the following step to get the docker container ID 

docker1 ps -a  

Now you should log into docker container to create and configure a MySQL database. 
# first login to docker container, replace xxxxxxx with the container ID you got from last step

docker1 exec -it xxxxxxx /bin/sh

#Now you are in Docker container. In BioHPC's implementation of Docker, /workdir/MyUserID on the host machine is mapped to /workdir within container.  

#Ceate database with the following command, and replace some_db_name_radtags with your database name. Te database name must have “_radtags” suffix.

create database some_db_name_radtags

mysql some_db_name_radtags < /usr/local/share/stacks/sql/stacks.sql 

#load database following instruction at http://catchenlab.life.illinois.edu/stacks/comp/load_radtags.php

e.g

load_radtags.pl  -D some_db_name_radtags -b 1 -p /workdir/redseq_experiment/stacks/ -B -e "This is our Experiment batch 1" -c

 

 

5. Now you can exit docker by command "exit".

 

6. To view the results after the calculation is completed (or after the results obtained elsewhere are loaded in MySQL),  open any web browser  and navigate to http://cbusxxxxx.tc.cornell.edu:8009/stacks/index.php. (For off campus computer, you will need to VPN into Cornell)

6. Your database(s) is subject to deletion once your reservation is over. To save the database for future use, you will have to copy the  /workdir/MyUserID/mysql  to your home directory which can be used later in a new reservation.


cp -r /workdir/MyUserID/mysql /home/MyUserID/
cp -r /workdir/MyUserID/export /home/MyUserID/


 

 


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