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Overview

All POD compute servers have identical Ubuntu 18.04 Operating System configurations.

A number of additional tools and packages have been installed on all compute servers, as listed below. Note that some tools that have many sub-program binaries, or for which multiple versions are installed,  are not available on the standard PATH. The /stor/system/opt directory on your system contains installation directories for these tools, which can be added to your PATH as needed.

Some PODs also have additional software installed which is unique to that POD.

Let us know if there is additional software you would like to have installed.

Web-based application R Studio and Python JupyterHub software

The following web application software is available on all PODs.  Accessing a POD node with your web browser will take you to an application login page where your BRCF account credentials can be used to access the application's web interface. Your default directory will be your Home directory. See Home directory quotas for important storage-quota related information. See also About R and R Studio Server.

SoftwareDescriptionAccess
JupyterHub Server
Python Notebook Server

Available on all compute servers

https://<server_name>.ccbb.utexas.edu
(e.g. https://gsafcomp01.ccbb.utexas.edu)

R Studio ServerR Studio Web Interface

The current version of R used for R Studio Server is R 3.6.1 on most compute servers. However R 4.0.3 is the R version on these compute servers:

Standard OS Software

(to find in repo: frep -r pattern .| grep -v /spec/)
SoftwareDescription
build-essentialgcc, g++, make, cmake, patch, autoconf, automake, m4, bison, libtool
emacs, vi, vim, edtext editors
postfixmail programs
perlperl interpretor
python 2python version 2 interpretor
python 3python version 3 interpretor
rubyruby programming language
sambaWindows SMB/CIFS file and printer sharing protocol and applications
screen, tmuxText window managers (multiplexer)
sshSecure Shell (remote access)
sudoRoot access for POD delegates only
tarFile archiving utility
wget, curlRemote file/url transfer utilities
gzip, zip, unzip

File compression and archiving tools.

sconsSoftware build tool
swigSoftware development tool
sqlite3SQL Lite databases
git
Version control utilities

Standard BioLinux Packages

(find using: dpkg -l bioperl) R modules in repo common.yaml
SoftwareVersionDescription
abyss

2.0.2-3

de novo, parallel, sequence assembler for short reads

bamtools

2.4.1+dfsg-2

toolkit for manipulating BAM (genome alignment) files

bedtools

2.26.0+dfsg-5

suite of utilities for comparing genomic features

bioperl

1.7.2-2

Perl tools for computational molecular biology

bioperl-run

1.7.1-3

BioPerl wrappers: scripts

blast2

1:2.6.0-1

Basic Local Alignment Search Tool

bowtie

1.2.2+dfsg-2

Ultrafast memory-efficient short read aligner

bowtie2

2.3.4.1-1

Ultrafast memory-efficient short read aligner

bwa0.7.17-1ubuntu0.1

Burrows-Wheeler Aligner

cd-hit

4.6.8-1

a suite of programs designed to quickly group sequences

clustalw

2.1+lgpl-5

No description

clustalx

2.1+lgpl-6

No description

cufflinks

2.2.1+dfsg.1-2

Transcript assembly, differential expression and regulation for RNA-Seq

ea-utils

1.1.2+dfsg-4build1

command-line tools for processing biological sequencing data

emboss

6.6.0+dfsg-6build1

european molecular biology open software suite

emboss-lib

6.6.0+dfsg-6build1

EMBOSS Libraries

fastdnaml

1.2.2-12

Tool for construction of phylogenetic trees of DNA sequences

fastqc

0.11.5+dfsg-6

A quality control application for high throughput sequence data

fastx-toolkit

0.0.14-5

FASTQ/A short nucleotide reads pre-processing tools

hmmer

3.1b2+dfsg-5ubuntu1

profile hidden Markov models for protein sequence analysis

jaligner

1.0+dfsg-4

Smith-Waterman algorithm with Gotoh’s improvement

jellyfish

2.2.8-3build1

count k-mers in DNA sequences

khmer

2.1.2+dfsg-3

k0.7.17-1ubuntu0.1-mer counting, filtering and graph traversal

libbiojava-java

1:1.7.1-7

Java API to biological data and applications (default version)

libbiojava-java-demos

1:1.7.1-7

Example programs for BioJava

macs

2.1.1.20160309-2

Model-based Analysis of ChIP-Seq on short reads sequencers

mafft

7.310-1

Multiple alignment program for amino acid or nucleotide sequences

maq

0.7.1-7

maps short fixed-length polymorphic DNA sequence reads to reference sequences

med-bio3.0.1ubuntu1Debian Med bioinformatics packages
med-cloud3.0.1ubuntu1

Debian Med bioinformatics applications usable in cloud computing

microbiomeutil

20101212+dfsg1-1build1

Microbiome Analysis Utilities

mothur

1.39.5-2build1

sequence analysis suite for research on microbiota

mothur-mpi

1.39.5-2build1

mpi-enabled binary for mothur

mrbayes-mpi

3.2.6+dfsg-2

Bayesian Inference of Phylogeny – mpi version

mummer

3.23+dfsg-3

Efficient sequence alignment of full genomes

muscle

1:3.8.31+dfsg-3

Multiple alignment program of protein sequences

ncbi-blast+

2.6.0-1

next generation suite of BLAST sequence search tools

ncbi-blast+-legacy

2.6.0-1

NCBI Blast legacy call script

ncbi-seg

0.0.20000620-4

tool to mask segments of low compositional complexity in amino acid sequences

ncbi-tools-bin

6.1.20170106-2

NCBI libraries for biology applications (text-based utilities)

ncbi-tools-x11

6.1.20170106-2

NCBI libraries for biology applications (X-based utilities)

paml

4.9g+dfsg-3

Phylogenetic Analysis by Maximum Likelihood (PAML)

parafly

0.0.2013.01.21-3build1

parallel command processing using OpenMP

phylip

1:3.696+dfsg-5

No description

phyml

3:3.3.20170530+dfsg-2

Phylogenetic estimation using Maximum Likelihood

picard-tools

2.8.1+dfsg-3

Command line tools to manipulate SAM and BAM files

primer3

2.4.0-1ubuntu2

Tool to design flanking oligo nucleotides for DNA amplification

pymol

1.8.4.0+dfsg-1build1

Molecular Graphics System

qiime

3:3.3.20170530+dfsg-2 (1.8.0+dfsg-4ubuntu1)?

Quantitative Insights Into Microbial Ecology

rasmol

2.7.5.2-2

Visualize biological macromolecules

raxml

8.2.11+dfsg-1

Randomized Axelerated Maximum Likelihood of phylogenetic trees

readseq

1-12

Conversion between sequence formats

rsem

1.2.31+dfsg-1

RNA-Seq by Expectation-Maximization

samtools

1.7-1

processing sequence alignments in SAM and BAM formats

sift

4.0.3b-6

predicts if a substitution in a protein has a phenotypic effect

sortmerna

2.1-2

tool for filtering, mapping and OTU-picking NGS reads

stacks

2.0Beta8c+dfsg-1

pipeline for building loci from short-read sequences

sumatra

1.0.31-1

fast and exact comparison and clustering of sequences

swarm

2.2.2+dfsg-1

robust and fast clustering method for amplicon-based studies

t-coffee

2.2.2+dfsg-1 (11.00.8cbe486-6)

Multiple Sequence Alignment

tophat

2.1.1+dfsg1-1

fast splice junction mapper for RNA-Seq reads

transdecoder

5.0.1-1

find coding regions within transcripts

trinityrnaseq

2.5.1+dfsg-2

RNA-Seq De novo Assembly

trnascan-se

1.3.1-1

search for tRNA genes in genomic sequences

velvet

1.2.10+dfsg1-3build1

Nucleic acid sequence assembler for very short reads

velvet-example

1.2.10+dfsg1-3build1

Example data for the Velvet sequence assembler

velvet-long

1.2.10+dfsg1-3build1

Nucleic acid sequence assembler for very short reads, long version

velvetoptimiser

2.2.6-1

Automatically optimise Velvet do novo assembly parameters

vsearch

2.7.1-1

tool for processing metagenomic sequences

zsh5.4.2-3ubuntu3.1shell with lots of features


Standard Third-Party Software (versions?)

SoftwareDescriptionVersion
R, RscriptR command-line shell and script execution programs.3.4.4, 3.5.3, 3.6.1
MatlabMathWorks Matlab Software.
See How do I use MATLAB on the POD?

dockerOS-level virtualization to deliver software in packages called containers
singularityContainerization software for scientific data

Additional Python Tools

(in repo under cqb-devel_tools/manifests/python.pp) find version with pip (pip3 freeze | grep xopen)
SoftwarePython2 VersionPython3 VersionDescription
all-dev


blaze0.10.10.10.1An interface to query data on different storage systems
cutadapt1.181.18Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads
dendropy

phylogenetic computing
freetype-dev (libfreetype6-dev)

This package contains all of the supplementary files you need to develop your own programs using the FreeType 2 library.
leukgen-disambiguate1.0.11.0.1Disambiguate reads mapping to multiple genomes. This is a frozen release with some bug fixes of the original AstraZeneca-NGS/disambiguate v1.0.
MACS22.1.2

Model Based Analysis for ChIP-Seq data

maplot1.0.21.0.2Python package for creating interactive MA-plots
matplotlib2.1.13.2.1python 2D plotting library
networkx2.22.0Creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
nimfa1.3.41.3.4Nonnegative matrix factorization
numpy1.13.31.13.3scientific computing with Python
pandas0.22.00.22.0Python Data Analysis Library
patsy0.4.1+dev0.2.1Patsy is a Python library for describing statistical models (especially linear models, or models that have a linear component) and building design matrices. Patsy brings the convenience of R “formulas” to Python.
pip

Python installation program (to install python modules)
plotly4.0.04.0.0

An open-source, interactive data visualization library for Python

pysam0.8.40.8.4a python module for reading, manipulating and writing genomic data sets
pyvttbl0.5.2.20.5.2.2Multidimensional pivot tables, data processing, statistical computation
reportlab (->biopython?)

3.4.0

(->1.70)

3.5.12 (->1.73)The ReportLab Toolkit. An Open Source Python library for generating PDFs and graphics. (→ Freely available tools for computational molecular biology)
rpy22.8.62.9.2Python interface to R
seaborn0.8.10.8.1statistical data visualization
scipy0.19.10.19.1Collection of Python software for mathematics, science, and engineering.
sklearn

Machine Learning in Python
skimage

Image processing in Python
statsmodels0.8.00.8.0Estimation of statistical models
pytorch/torch1.7.01.7.0Optimized tensor library for deep learning

torchvision

0.8.10.8.1popular datasets, model architectures, and common image transformations for computer vision


Additional R Tools

(in repo cqbhiera/common.yaml)
SoftwareDescription
abind

GNU R package “Combine multi-dimensional arrays”

ade4

GNU R package “Analysis of Ecological Data : Exploratory

ape

GNU R package “Analyses of Phylogenetics and Evolution”

bitops

GNU R package implementing bitwise operations

blogdownCreate Blogs and Websites with R Markdown
bookdown

Authoring Books and Technical Documents with R Markdown

catools

GNU R package “Tools: moving window statistics, GIF,

carCompanion to Applied Regression
cargo

cluster

GNU R package for cluster analysis by Rousseeuw et al

colourpicker

 A Colour Picker Tool for Shiny and for Selecting Colours in Plots

cowplot

Streamlined Plot Theme and Plot Annotations for 'ggplot2'

curlA Modern and Flexible Web Client for R

data.table

GNU R package “Extension of data.frame”

dbi

GNU R package “R Database Interface”

dbplyrR Database Interface
dendextendExtending 'dendrogram' Functionality in R

dichromat

Color schemes for dichromats

digest

GNU R package “Create Cryptographic Hash Digests of R

emmeans

Estimated Marginal Means, aka Least-Squares Means

evaluate

GNU R package “Parsing and Evaluation Tools that Provide

fivethirtyeight

Data and Code Behind the Stories and Interactives at 'FiveThirtyEight'

forcats

Data and Code Behind the Stories and  Interactives at 'FiveThirtyEight'

foreachProvides Foreach Looping Construct

futile.logger

GNU R package “A Logging Utility for R”

futile.options

GNU R package “Futile options management”

gdata

GNU R package “Various R Programming Tools for Data

getopt

GNU R package “C-like getopt behavior.”

gganimateA Grammar of Animated Graphics
GGallyExtension to 'ggplot2'
ggExtra

Add Marginal Histograms to 'ggplot2', and More 'ggplot2' Enhancements

ggplot2

GNU R package “An Implementation of the Grammar of

ggpubr'ggplot2' Based Publication Ready Plots
ggrepel

Automatically Position Non-Overlapping Text Labels with 'ggplot2'

ggsci

Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'

ggsignifSignificance Brackets for 'ggplot2'
gifskiHighest Quality GIF Encoder
glmnet

Lasso and Elastic-Net Regularized Generalized Linear Models

gplots

GNU R package “Various R Programming Tools for Plotting

gridSVGExport 'grid' Graphics as SVG
gtBuild display tables from tabular data with an easy-to-use set of functions

gtable

GNU R package “Arrange grobs in tables.”

gtools

GNU R package “Various R Programming Tools”

haven

Import and Export 'SPSS', 'Stata' and 'SAS' Files

igraphNetwork Analysis and Visualization
interactions

Comprehensive, User-Friendly Toolkit for Probing Interactions

jpegRead and write JPEG images

labeling

GNU R package “Axis Labeling”

lambda.r

GNU R package “Modeling Data with Functional Programming”

lattice

GNU R package “Lattice Graphics”

latticeExtraExtra Graphical Utilities Based on Lattice
leaps

GNU R package “regression subset selection”

libssl-devprereq?
libcairo2-devperreq?
libxt-devprereq?
libgmp10prereq?
libgmp-devprereq?
libmpfr6prereq?
libmpfr-devprereq?
lme4

GNU R package for linear mixed effects model fitting

locfit

Local Regression, Likelihood and Density Estimation

lubridateMake Dealing with Dates a Little Easier

matrix

GNU R package of classes for dense and sparse matrices

matrixstats

R package “Methods that apply to rows and columns of a matrix”

mirbase.dbmiRBase: the microRNA database
mixdistFinite Mixture Distribution Models
modelr

Modelling Functions that Work with the Pipe

multcomp

Simultaneous Inference in General Parametric Models

munsell

GNU R package “Munsell colour system”

mvtnormMultivariate Normal and t Distributions
networkClasses for Relational Data

nlme

GNU R package for (non-)linear mixed effects models

nloptrR Interface to NLopt
ontologyIndexFunctions for Reading Ontologies into R

optparse

GNU R package “Command line option parser.”

permute

GNU R package “Functions for Generating Restricted

pheatmapPretty Heatmaps
pbkrtest

Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison

plotlyCreate Interactive Web Graphics via 'plotly.js'
plotROC

Generate Useful ROC Curve Charts for Print and Interactive Use

plotrix

GNU R package “Various plotting functions”

plyr

GNU R package “Tools for Splitting, Applying and Combining

polynom

A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations

proto

GNU R package “Prototype object-based programming”

quantmodQuantitative Financial Modelling Framework
quantregQuantile Regression

r.methodss3

GNU R package “Utility function for defining S3 methods”

rcolorbrewer

GNU R package providing suitable color palettes

rcpp

GNU R package “Seamless R and C++ Integration”

rcurl

GNU R package “General Network (HTTP/FTP/…) Client

relimp

GNU R package “Relative Contribution of Effects in a

reshape2

GNU R package “Flexibly Reshape Data: A Reboot of the

reticulateInterface to 'Python'

rggobi

GNU R package for the GGobi data visualization system

rgl

GNU R package for three-dimensional visualisation using OpenGL

rgtk2

GNU R binding for Gtk2

rmpi

GNU R package interfacing MPI libraries for distributed computing

RMySQLDatabase Interface and 'MySQL' Driver for R
ROCR

Visualizing the Performance of Scoring Classifiers

rserve

GNU R Rserve tcp/ip server and sample clients

rstatix

Pipe-Friendly Framework for Basic Statistical Tests

rsqlite

GNU R package “SQLite Interface for R”

rvestEasily Harvest (Scrape) Web Pages

scales

GNU R package “Scale Functions for Visualization”

scatterplot3d

GNU R package “3D Scatter Plot”

servr

A Simple HTTP Server to Serve Static Files or Dynamic Documents

SeuratTools for Single Cell Genomics
shapeFunctions for Plotting Graphical Shapes, Colors
shinyWeb Application Framework for R
shinyjs

Easily Improve the User Experience of Your Shiny Apps in Seconds

showtextMaking it easy to use various types of fonts in R graphs
showtextdbProviding font files that can be used by the 'showtext' package
SignacA framework for the analysis of single-cell chromatin data
snaTools for Social Network Analysis

sp

GNU R package “Classes and Methods for Spatial Data”

sqldfManipulate R Data Frames Using SQL
statnet.common

Common R Scripts and Utilities Used by the Statnet Project Software

stringr

GNU R package “Simple, Consistent Wrappers for Common

sysfontsLoading system fonts and Google Fonts into R

tcltk2

GNU R package “Tcl/Tk Additions”

testthat

GNU R package “Testthat code. Tools to make testing fun

tibbleSimple Data Frames
tidyrTidy Messy Data
tidyverseEasily Install and Load the 'Tidyverse'
transformrPolygon and Path Transformations

vegan

GNU R package “Community Ecology Package”

VennDiagramGenerate High-Resolution Venn and Euler Plots
VGAMVector Generalized Linear and Additive Models
vioplotViolin Plot
xfunMiscellaneous Functions by 'Yihui Xie'

xml

GNU R package “Tools for Parsing and Generating XML Within

xtable

GNU R coerce data to LaTeX and HTML tables

Additional R BioConductor Tools

(in repo cqbhiera/common.yaml)
SoftwareDescription
affyMethods for Affymetrix Oligonucleotide Arrays
affyio

GNU R package “Tools for parsing Affymetrix data files”

annotate

GNU R package “Annotation for microarrays”

annotationdbi

GNU R package “Annotation Database Interface”

arrayQualityMetricsQuality metrics report for microarray data sets
ballgownFlexible, isoform-level differential expression analysis
biobase

GNU R package “Biobase: Base functions for Bioconductor”

biocgenerics

GNU R package “S4 generic functions for Bioconductor”

biocinstaller

GNU R package “Install/Update Bioconductor and CRAN

biocparallel

GNU R package “Bioconductor facilities for parallel

biomart

GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)

biostrings

GNU R package “String objects representing biological

BSgenomeEfficient genome searching
BSgenome.Hsapiens.UCSC.hg19

Full genome sequences for Homo sapiens (UCSC version hg19)

ChIPseekerannotating ChIP-seq data analysis
cummeRbundanalyzing Cufflinks RNA-Seq output
deseq
DESeq2Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution
devtools

Collection of package development tools

DEXSeqfinding differential exon usage using RNA-seq exon counts between samples
EnhancedVolcanoPublication-ready volcano plots with enhanced colouring and labeling
genefilter

GNU R package “genefilter: methods for filtering genes

geneplotter

Graphics related functions for Bioconductor

genomeinfodb

GNU R package “Utilities for manipulating chromosome and

genomicalignments

GNU R package “Representation and manipulation of short

genomicranges

GNU R package “Representation and manipulation of genomic

ggplot2moviesMovies Data
GISPA

GISPA: Method for Gene Integrated Set Profile Analysis

GOstatstools for interacting with GO and microarray data
GO.db

hilbertvis

GNU R package to visualise long vector data

httpuvHTTP and WebSocket Server Library

iranges

GNU R package “Infrastructure for manipulating intervals

JunctionSeq

JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data

limma

GNU R package “Linear Models for Microarray Data”

mirbase.dbmiRBase: the microRNA database

multtest

GNU R package “Resampling-based multiple hypothesis

org.Hs.eg.dbGenome wide annotation for Human
org.Sc.sgd.dbGenome wide annotation for Yeast
org.Mm.eg.dbGenome wide annotation for Mouse
org.Rn.eg.dbGenome wide annotation for Rat

preprocesscore

GNU R package “A collection of pre-processing functions”

processxExecute and Control System Processes
pkgload
qvalue

Bioconductor package “Q-value estimation for false discovery rate control”

rhdf5

provides an interface between HDF5 and R

readrRead Rectangular Text Data
ReportingToolsTools for making reports in various formats
RIPSeekeridentify protein-associated transcripts from RIP-seq experiments
roxygen2In-Line Documentation for R
rsamtools

GNU R package “Binary alignment (BAM), variant call (BCF),

s4vectors

GNU R package “S4 implementation of vectors and lists”

SISPA

SISPA: Method for Sample Integrated Set Profile Analysis

sleuthanalysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto
ShortReadsampling, iteration, and input of FASTQ files
topGOEnrichment Analysis for Gene Ontology
TxDb.Scerevisiae.UCSC.sacCer3.sgdGeneAnnotation package for TxDb object(s)
TxDb.Hsapiens.UCSC.hg38.knownGeneAnnotation package for TxDb object(s)
tximport

Import and summarize transcript-level estimates for transcript- and gene-level analysis

WGCNAWeighted Correlation Network Analysis

xvector

GNU R package “Representation and manpulation of external

yardstickTidy Characterizations of Model Performance

zlibbioc

GNU R package “An R packaged zlib-1.2.5″

Additional Perl CPAN modules

(in repo cqbprofile/manifest/perl.pp and cqb-maker)
SoftwareDescription
Bit::Vector
CGI
DBI
DBD::SQLite
File::Which
forks
forks::shared
Graph
IO::All
IO:Prompt
LWP
Math::Cephes
Module::Build
Net::HTTP
Perl::Unsafe::Signals
Statistics::Descriptive
Switch
Test::Class
Test::More
Test::Exception
Test::Harness
XML::Simple

Next Generation Sequencing (NGS) Tools

(in repo cqbprofile/manifest/next_gen_sequencing_client.pp)
SoftwareDescriptionPath
bamtoolsSAM/BAM file manipulation/stor/system/opt/gitdir/bamtools/bin/bamtools
bcl2fastqBCL file manipulation/usr/bin/bcl2fastq
deeptools

enabrowsertools

hisat

fastq_screen

guppy

samtoolsSAM/BAM file manipulation/usr/bin/samtools
/usr/bin/samtools_0.1.18
/usr/bin/samtools-1.3
picardSAM/BAM file manipulation/stor/system/opt/picard-tools-1.141
/stor/system/opt/picard-tools-2.5.0

bedtools

BED/GFF file manipulation/usr/bin/bedtools-2.17.0
/usr/bin/bedtools-2.25.0
samtools

scalangs

sra toolkitSRA file manipulation/stor/system/opt/sratoolkit.2.7.0-ubuntu64
stringtie

bwaAlignment

/usr/bin/bwa
/usr/bin/bwa-0.5.9
/usr/bin/bwa5
/usr/bin/bwa-0.6.2
/usr/bin/bwa6

RNA Sequencing Tools

(in repo cqbprofile/manifest/rna_sequencing_client.pp)
SoftwareDescriptionPath
augustusprogram to find genes and their structures in one or more genomes
busco

cellranger

cufflinks

expressExpression quantification/usr/bin/express
fastqc

featurecountsCounting/usr/bin/featureCounts
htseqCounting/stor/system/opt/HTSeq-0.6.1p1
kallistoExpression quantification/usr/bin/kallisto
STARAlignment/usr/bin/STAR
/usr/bin/STARlong
tophat

MultiQCReport Generation/usr/bin/multiqc
RNA-SeQCQC of RNA-seq alignments. To run this Java program:
java -jar /stor/system/opt/rnaseqc/RNA-SeQC_v1.1.8.jar <other options>
/stor/system/opt/rnaseqc
salmon

hisatSpliced alignment for mapping RNA-seq reads/stor/system/opt/hisat-0.1.6-beta
hisat2Align NGS reads (both DNA and RNA) against a reference genome/stor/system/opt/hisat2-2.0.5/
gossamerbioinformatics suite including goss, gossple, xenome, and electus

/usr/local/bin/goss

/usr/local/bin/gossple

/usr/local/bin/xenome

/usr/local/bin/electus

Specialized NGS Tools

(in repo specialized_sequencing_client.pp)
SoftwareDescriptionPath
BWA

bwa_mem2

MultiQCReport Generation/usr/bin/multiqc
eisen clusterhierachical & k-means clustering/usr/bin/cluster-eisen
imageJ

meme suitemotif analysis/stor/system/opt/meme_4.11.2
meme_chipmotif analysis suite for ChIP-seq/stor/system/opt/software/meme-chip/4.11.2/
artnext generation sequencing read simulator/usr/bin/art_454
/usr/bin/art_illumina
/usr/bin/art_SOLiD

Variant Analysis Tools (variant_analysis_client.pp)

NB: These tools are only available on select PODs.  At this time of this writing, it included the GSAF and Iyer PODs.

SoftwareDescriptionPath
annovarAnnotation of variants/stor/system/opt/annovar/
gatkHuman/higher-vertabrate variant detection toolkit/stor/system/opt/gatk-3.6/
MuTectSomatic Mutations/stor/system/opt/gatk-3.6/
/stor/system/opt/mutect/
plink

GWAS tools

/usr/bin/plink
snpeffGenetic variant annotation and effect prediction/stor/system/opt/snpEff

Evolutionary Analysis Tools (evolution_sequencing_client.pp)

Note: These tools are only available on select PODs.  At this time of this writing, it included the GSAF POD.

SoftwareDescriptionPathin evolution_sequencing_client.pp?
mauve

y

Genome/Transcriptome Assembly Tools genome_client.pp

Note: These tools are only available on select PODs.  At this time of this writing, it included the GSAF and Educational PODs.

SoftwareDescriptionPath
consedcontig assembly tools/usr/local/genome/consed/
phrapcontig assembly tools/usr/local/genome/bin/
phredcontig assembly tools/usr/local/genome/bin/
glimmermicobial gene annotations/usr/bin/glimmer2
/usr/bin/build-icm
/usr/bin/extract
/usr/bin/long-orfs
ISEScanidentification of insertion sequence elements in genomes/usr/lib/libssw.so
FragGeneScanrequirement of ISEScan/usr/bin/FragGeneScan1.30

Molecular Structures Client

SoftwareDescriptionPath
gromacspackage to perform molecular dynamics
mgltools

software for visualization and analysis of

molecular structures


nwchemcomputes properties of molecular and periodic systems


Other software Packages

SoftwareDescripitionPathpuppet file
tensorflowplatform for machine learningpythoncompute_server.pp
kerashigh-level API of TensorFlowpythoncompute_server.pp


POD-specific software (look for these)

The following software is available only on specific PODs or nodes of a pod.

SoftwareDescriptionLocationPath
bam2fastq
Iyer POD/stor/system/opt/bam2fastq-1.1.0/
basespace
GSAF POD
canu
Chen POD
crossstitch
Ochman POD
falcon
Chen POD
irodsfsNot yet fully supportedgsafcbig01/mnt/corral
maker
Ochman POD
R bitops


R caTools
Iyer POD
R snow
Iyer POD
R Snowfall


R phantompeakqualtools
Iyer POD
R NCIS
Iyer POD
volalign
Marcotte POD

3.6.1

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