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BioHPC Lab:
User Guide

 


BioHPC Lab Software

There is 391 software titles installed in BioHPC Lab. 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 Lab.

454 gsAssembler or gsMapper, a5, ABruijn, ABySS, AdapterRemoval, Admixtools, Admixture, albacore, Alder, AlleleSeq, ALLMAPS, ALLPATHS-LG, AMOS, AMPHORA, analysis, ANGSD, Annovar, apollo, Atlas-Link, ATLAS_GapFill, ATSAS, Augustus, bamtools, Basset, BayeScan, BBmap, BCFtools, bcl2fastq, Beagle, Beagle4, Beast2, bedops, BEDtools, bfc, bgc, biobambam, Bioconductor, BioPerl, BioPython, Birdsuite, Bismark, blasr, BLAST, blast2go, BLAT, bmtagger, Boost, Bowtie, Bowtie2, breseq, BSseeker2, BUSCO, BWA, canu, CAP3, CBSU RNAseq, cd-hit, CEGMA, CellRanger, CheckM, Circos, Circuitscape, CLUMPP, Clustal Omega, CLUSTALW, Cluster, cmake, CNVnator, cortex_var, CrossMap, CRT, cuda, Cufflinks, cutadapt, dadi, dadi-1.6.3_modif, dDocent, DeconSeq, deepTools, delly, destruct, DETONATE, diamond, Discovar, Discovar de novo, distruct, Docker, dREG, Drop-seq, dropSeqPipe, dsk, ea-utils, ecopcr, EDGE, EIGENSOFT, EMBOSS, entropy, ermineJ, exabayes, exonerate, eXpress, FALCON, FALCON_unzip, Fast-GBS, fasta, FastML, fastq_species_detector, FastQC, fastStructure, FastTree, FASTX, fineSTRUCTURE, flash, Flexible Adapter Remover, FMAP, freebayes, FunGene Pipeline, GATK, GBRS, GCTA, GEM library, GEMMA, geneid, GeneMark, GeneMarker, Genome STRiP, GenomeMapper, GenomeStudio (Illumina), GenomicConsensus, gensim, germline, GMAP/GSNAP, GNU Compilers, GNU parallel, Grinder, GROMACS, Gubbins, HapCompass, HAPCUT, HAPCUT2, hapflk, HaploMerger, Haplomerger2, HapSeq2, HiC-Pro, HISAT2, HMMER, Homer, HOTSPOT, HTSeq, HUMAnN2, HyPhy, iAssembler, IBDLD, IDBA-UD, IGV, IMa2, IMa2p, IMAGE, impute2, infernal, InStruct, InteMAP, InterProScan, iRep, java, jbrowse, jellyfish, JoinMap, julia, jupyter, kallisto, Kent source utilities, khmer, LACHESIS, lcMLkin, LDAK, leeHom, LINKS, LocusZoom, longranger, LUCY, LUCY2, LUMPY, MACS, MaCS simulator, MACS2, MAFFT, Magic-BLAST, MAKER, MAQ, MASH, MaSuRCA, Mauve, mccortex, megahit, MEGAN, MEME Suite, MERLIN, MetaBAT, metaCRISPR, MetAMOS, MetaPathways, MetaPhlAn, MetaVelvet, MetaVelvet-SL, Migrate-n, mira, miRDeep2, MISO (misopy), MixMapper, MKTest, MMSEQ, mothur, MrBayes, mrsFAST, msld, MSMC, MSR-CA Genome Assembler, msstats, MSTMap, mugsy, MultiQC, MUMmer, muscle, muTect, ncftp, Nemo, Netbeans, NEURON, new_fugue, NextGenMap, NGSadmix, ngsDist, ngsF, ngsTools, NGSUtils, Novoalign, NovoalignCS, Oases, OBITools, Orthomcl, PAGIT, PAML, pandas, pandaseq, Panseq, PASA, PASTEC, pbalign, pbh5tools, PBJelly, PBSuite, PeakSplitter, PEAR, PennCNV, ph5tools, Phage_Finder, PHAST, PHYLIP, PhyloCSF, phylophlan, PhyML, Picard, Pindel, piPipes, PIQ, Platypus, plink, Plotly, popbam, prinseq, prodigal, progressiveCactus, prokka, pyRAD, PySnpTools, PyVCF, QIIME, QIIME2 q2cli, Quake, QuantiSNP2, QUAST, QUMA, R, RACA, RADIS, RAPTR-SV, RAxML, Ray, Rcorrector, REAPR, RepeatMasker, RepeatModeler, RFMix, RNAMMER, rnaQUAST, Roary, RSEM, RSeQC, RStudio, sabre, SaguaroGW, samblaster, Samtools, Satsuma, scikit-learn, scythe, Sentieon, SeqPrep, sgrep, SHAPEIT, shore, SHOREmap, shortBRED, SHRiMP, sickle, SignalP, simuPOP, skewer, smcpp, SMRT Analysis, snakemake, snap, SNAPP, SNPhylo, SOAP2, SOAPdenovo, SOAPdenovo-Trans, SOAPdenovo2, SomaticSniper, SPAdes, SRA Toolkit, srst2, stacks, stampy, STAR, statmodels, Strelka, StringTie, STRUCTURE, supernova, SURPI, sutta, SVDetect, svtools, SweepFinder, sweepsims, tabix, Tandem Repeats Finder (TRF), TASSEL 3, TASSEL 4, TASSEL 5, tcoffee, TensorFlow, TEToolkit, TMHMM, TopHat, traitRate, Trans-Proteomic Pipeline (TPP), TransComb, TransDecoder, transrate, TRAP, treeCl, treemix, trimmomatic, Trinity, Trinotate, tRNAscan-SE, UCSC Kent utilities, UMI-tools, usearch, Variant Effect Predictor, VarScan, vcf2diploid, vcfCooker, vcflib, vcftools, Velvet, VESPA, ViennaRNA, VIP, VirusFinder 2, VizBin, vsearch, WASP, wgs-assembler (Celera), Wise2 (Genewise), Xander_assembler, yaha

Details for stacks (hide)

Name:stacks
Version:1.44
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:11/1/2016 6:57:36 AM
Link:http://creskolab.uoregon.edu/stacks/
Platform:Ilumina
Notes:

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. Output directories created by these programs can then be transferred to a machine equipped with MySQL and the apache web server and uploaded to MySQL using the script load_radtags.pl.

MySQL and apache are functional on cbsuwrkst2, cbsuwrkst3, cbsuwrkst4, cbsulm01, and cbsulm04. These machines can be used both for the computational part of Stacks run, as well as for visualization and data analysis following the computational part. 

Prior to loading your Stacks results into MySQL database on one of the selected machines listed above (or prior to running Stacks scripts without the "-S" option on these machines) you will have to prepare the SQL database. First, copy the file .my.cnf into your HOME directory (this needs to be done only once):

cd
cp /programs/stacks/share/stacks/sql/.my.cnf .


Check for old databases that may have been left over by previous users:

mysql -e "show databases"

Any database whose name ends with "_radtags" and does not belong to you can be deleted to save disk space:

mysql -e "drop database SOMENAME_radtags"

Now you should create and configure a MySQL database for your project using the following two commands (remember that the database name has to have “_radtags” suffix):

mysql -e "create database some_db_name_radtags"
mysql some_db_name_radtags < /programs/stacks/share/stacks/sql/stacks.sql


To view the results after the calculation is completed (or after the results obtained elsewhere are loded in MySQL), open the web browser (firefox) on the machine where the MySQL database is located (not on your laptop!) and navigate to http://localhost/stacks/index.php.

Your database(s) is subject to deletion once your reservation is over. To save the database for future use, you will have to export it to a file (preferably in compressed format) located somewhere in your home directory, e.g.,

mysqldump MYDB_radtags | gzip -c > /home/my_login_id/MYDB_radtags.sql.gz

where my_login_id is your login ID and MYDB is the first part of the database name. The file saved this way can later be imported to MySQL on the same or on a diferent machine using the commands

mysql -e "create database MYDB_radtags"
gzip -d -c /home/my_login_id/MYDB_radtags.sql.gz | mysql MYDB_radtags


When you are done with your project, before logging out, please be courteous to other users and clean up your databases from MySQL using the "drop database" command, e.g.,

mysql -e "drop database MYDB_radtags" 
 


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