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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 MetaPathways (hide)

About:MetaPathways v2.5 is a meta'omic analysis pipeline for the annotation and analysis for environmental sequence information.
Added:9/21/2016 3:40:39 PM

MetaPathways has to be run in graphical environemnt. i.e., you either need to be connected throu VNC, or your ssh clinet has to have X11 ports forwarded and an X-windows manager has to be running on the machine you are connectiing from (e.g.,  your laptop). Please refer to a description of graphical access options in our User Guide: remote access instructions.

Before running MetaPathways you need to set up program environment by running


Create the directory pgdbs (needed by pathway-tools) in /workdir and make it wolrd-writeable:

mkdir /workdir/pgdbs

chmod a+rwx /workdir/pgdbs

Prepare the BLAST/LAST database directory in /workdir:

rsync -av /programs/MetaPathways/MetaPathways_DBs /workdir

In /workdir, create a directory for the run, for example (replace myID with your own userID):

mkdir -p /workdir/myID/my_run

Copy run configuration file to this new directory:

cd /workdir/myID/my_run

cp /programs/MetaPathways/metapathways2-2.5.1/config/*.txt .

If needed, edit the file template_param.txt and set your preferred databases and run parameters (the file template_config.txt does not have to be edited if the database and pgdbs directories have been created as described above).

Place your input fasta files in /workdir/myID/my_run.

Create the output directory for the run, e.g.:

mkdir -p /workdir/myID/my_run/out

Launch the program's GUI interface by typing

/programs/MetaPathways/bin/MetaPathways2 &

which will make a window pop up. NOTE: The GUI interface, although it needs to stay open, does not work correctly and will not be used to initiate the actual analysis. While the GUI can still be used to view the results, the actual run has to be launched in command-line mode, similar to the following (see manual for details):


source /programs/MetaPathways/metapathways2-2.5.1/MetaPathwaysrc

python /programs/MetaPathways/metapathways2-2.5.1/ -i /workdir/myID/my_run/ -o /workdir/myID/my_run/out/ -c ./template_config.txt -p ./template_param.txt -v -r overlay -s my_input >& run.log

The first of the commands above sets the environment for the run, while the second command launches Metapathways. In the example above, it is assumed that the input file names start with my_input, .i.e.., my_input.fasta. For convenience, the two commands can be placed in a shell script (say,, which can then be easily modified for other runs. The screen output from the second command will be saved on disk in the file run.log.

NOTE: In the final stages of the run, pathway-tools program (called from withn Metapathways) will attempt to temporarily display and then close a few graphical windows, which is the reason why the program needs to be run in graphical environment even though the GUI interface is not being used.

After the run completes, the results, created in directory structure under /workdir/myID/my_run/out, can be visualized using the Methapathways GUI (which was launched in the beginning and is already running in the background).

NOTE on databases: you can add more databases to /workdir/MetaPathways_DBs. Just deposit the fasta file in the proper subdirectory (functional or taxonomic), add the name of the fasta file to the proper database line in template_params.txt. During the run the new database will (or at least should) be formatted and searched. It can also be formatted manually before MetaPathways run, although the details of the formatting command are not yet given in Metapathways description. 


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