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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/software/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 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

Standard OS Software (where 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, unzipFile compression and archiving tools.

Standard BioLinux Packages (how check versions? dpkg -l bioperl) check R modules in common.yaml

SoftwareVersionDescriptionin cqb-biolinux?
abyss

2.0.2-3

de novo, parallel, sequence assembler for short reads

y

bamtools

2.4.1+dfsg-2

toolkit for manipulating BAM (genome alignment) files

y

bedtools

2.26.0+dfsg-5

suite of utilities for comparing genomic features

y
bioperl

1.7.2-2

Perl tools for computational molecular biology

y

bioperl-run

1.7.1-3

BioPerl wrappers: scripts

y
blast2

1:2.6.0-1

Basic Local Alignment Search Tool

y
bowtie

1.2.2+dfsg-2

Ultrafast memory-efficient short read aligner

y
bowtie2

2.3.4.1-1

Ultrafast memory-efficient short read aligner

n
bwa0.7.17-1ubuntu0.1

Burrows-Wheeler Aligner

n
cd-hit

4.6.8-1

a suite of programs designed to quickly group sequences

y

clustalw

2.1+lgpl-5

No description

y

clustalx

2.1+lgpl-6

No description

y

cufflinks

2.2.1+dfsg.1-2

Transcript assembly, differential expression and regulation for RNA-Seq

n

ea-utils

1.1.2+dfsg-4build1

command-line tools for processing biological sequencing data

y

emboss

6.6.0+dfsg-6build1

european molecular biology open software suite

n

emboss-lib

6.6.0+dfsg-6build1

EMBOSS Libraries

y

fastdnaml

1.2.2-12

Tool for construction of phylogenetic trees of DNA sequences

y

fastqc

0.11.5+dfsg-6

A quality control application for high throughput sequence data

n

fastx-toolkit

0.0.14-5

FASTQ/A short nucleotide reads pre-processing tools

y

hmmer

3.1b2+dfsg-5ubuntu1

profile hidden Markov models for protein sequence analysis

n

jaligner

1.0+dfsg-4

Smith-Waterman algorithm with Gotoh’s improvement

y

jellyfish

2.2.8-3build1

count k-mers in DNA sequences

y

khmer

2.1.2+dfsg-3

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

y

libbiojava-java

1:1.7.1-7

Java API to biological data and applications (default version)

y

libbiojava-java-demos

1:1.7.1-7

Example programs for BioJava

y

macs

2.1.1.20160309-2

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

y

mafft

7.310-1

Multiple alignment program for amino acid or nucleotide sequences

y

maq

0.7.1-7

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

y
med-bio3.0.1ubuntu1Debian Med bioinformatics packagesy
med-cloud3.0.1ubuntu1

Debian Med bioinformatics applications usable in cloud computing

y

microbiomeutil

20101212+dfsg1-1build1

Microbiome Analysis Utilities

y

mothur

1.39.5-2build1

sequence analysis suite for research on microbiota

y

mothur-mpi

1.39.5-2build1

mpi-enabled binary for mothur

y

mrbayes-mpi

3.2.6+dfsg-2

Bayesian Inference of Phylogeny – mpi version

y

mummer

3.23+dfsg-3

Efficient sequence alignment of full genomes

y

muscle

1:3.8.31+dfsg-3

Multiple alignment program of protein sequences

y

ncbi-blast+

2.6.0-1

next generation suite of BLAST sequence search tools

n

ncbi-blast+-legacy

2.6.0-1

NCBI Blast legacy call script

n

ncbi-seg

0.0.20000620-4

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

y

ncbi-tools-bin

6.1.20170106-2

NCBI libraries for biology applications (text-based utilities)

y

ncbi-tools-x11

6.1.20170106-2

NCBI libraries for biology applications (X-based utilities)

y

paml

4.9g+dfsg-3

Phylogenetic Analysis by Maximum Likelihood (PAML)

y

parafly

0.0.2013.01.21-3build1

parallel command processing using OpenMP

y

phylip

1:3.696+dfsg-5

No description

y

phyml

3:3.3.20170530+dfsg-2

Phylogenetic estimation using Maximum Likelihood

y

picard-tools

2.8.1+dfsg-3

Command line tools to manipulate SAM and BAM files

y

primer3

2.4.0-1ubuntu2

Tool to design flanking oligo nucleotides for DNA amplification

y

pymol

1.8.4.0+dfsg-1build1

Molecular Graphics System

y

qiime

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

Quantitative Insights Into Microbial Ecology

y

rasmol

2.7.5.2-2

Visualize biological macromolecules

y

raxml

8.2.11+dfsg-1

Randomized Axelerated Maximum Likelihood of phylogenetic trees

y

readseq

1-12

Conversion between sequence formats

y

rsem

1.2.31+dfsg-1

RNA-Seq by Expectation-Maximization

y

samtools

1.7-1

processing sequence alignments in SAM and BAM formats

n

sift

4.0.3b-6

predicts if a substitution in a protein has a phenotypic effect

y

sortmerna

2.1-2

tool for filtering, mapping and OTU-picking NGS reads

y

stacks

2.0Beta8c+dfsg-1

pipeline for building loci from short-read sequences

y

sumatra

1.0.31-1

fast and exact comparison and clustering of sequences

y

swarm

2.2.2+dfsg-1

robust and fast clustering method for amplicon-based studies

y

t-coffee

2.2.2+dfsg-1 (11.00.8cbe486-6)

Multiple Sequence Alignment

n

tophat

2.1.1+dfsg1-1

fast splice junction mapper for RNA-Seq reads

n

transdecoder

5.0.1-1

find coding regions within transcripts

y

trinityrnaseq

2.5.1+dfsg-2

RNA-Seq De novo Assembly

y

trnascan-se

1.3.1-1

search for tRNA genes in genomic sequences

y

velvet

1.2.10+dfsg1-3build1

Nucleic acid sequence assembler for very short reads

y

velvet-example

1.2.10+dfsg1-3build1

Example data for the Velvet sequence assembler

y

velvet-long

1.2.10+dfsg1-3build1

Nucleic acid sequence assembler for very short reads, long version

y

velvetoptimiser

2.2.6-1

Automatically optimise Velvet do novo assembly parameters

y

vsearch

2.7.1-1

tool for processing metagenomic sequences

y
zsh5.4.2-3ubuntu3.1shell with lots of featuresy


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?

Additional Development Tools (move to regular)

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

Additional Python Tools (cqb-devel_tools/manifests/python.pp) find version with pip (pip3 freeze | grep xopen)

SoftwarePython2 VersionPython3 VersionDescription

in devel_tools

all-dev


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

phylogenetic computingy
freetype-dev (libfreetype6-dev)

This package contains all of the supplementary files you need to develop your own programs using the FreeType 2 library.y
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.y
MACS22.1.2

Model Based Analysis for ChIP-Seq data

y
maplot1.0.21.0.2Python package for creating interactive MA-plotsy
matplotlib2.1.13.2.1python 2D plotting libraryy
networkx2.22.0Creation, manipulation, and study of the structure, dynamics, and functions of complex networks.y
nimfa1.3.41.3.4Nonnegative matrix factorizationy
numpy1.13.31.13.3scientific computing with Pythony
pandas0.22.00.22.0Python Data Analysis Libraryy
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.y
pip

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

An open-source, interactive data visualization library for Python

y
pysam0.8.40.8.4a python module for reading, manipulating and writing genomic data setsy
pyvttbl0.5.2.20.5.2.2Multidimensional pivot tables, data processing, statistical computationy
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)y
rpy22.8.62.9.2Python interface to Ry
seaborn0.8.10.8.1statistical data visualizationy
scipy0.19.10.19.1Collection of Python software for mathematics, science, and engineering.y
sklearn

Machine Learning in Pythony
skimage

Image processing in Pythony
statsmodels0.8.00.8.0Estimation of statistical modelsy


Additional R Tools (cqbhiera/common.yaml dont appear to have versions)

SoftwareDescription

in common.yaml

listed in library()
abind

GNU R package “Combine multi-dimensional arrays”

yy

ade4

GNU R package “Analysis of Ecological Data : Exploratory


y
ape

GNU R package “Analyses of Phylogenetics and Evolution”


y

bitops

GNU R package implementing bitwise operations


y
blogdownCreate Blogs and Websites with R Markdownyy
bookdown

Authoring Books and Technical Documents with R Markdown

yy

catools

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

yy
carCompanion to Applied Regressionyy
cargo
yn

cluster

GNU R package for cluster analysis by Rousseeuw et al


y
colourpicker

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

yy
cowplot
y
curl
y

data.table

GNU R package “Extension of data.frame”



dbi

GNU R package “R Database Interface”



dbplyr
y
dendextend


dichromat

Color schemes for dichromats



digest

GNU R package “Create Cryptographic Hash Digests of R



emmeans
y

evaluate

GNU R package “Parsing and Evaluation Tools that Provide



fivethirtyeight
y
forcats
y
foreach
y

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.”



gganimate
y
GGally
y
ggExtra
y

ggplot2

GNU R package “An Implementation of the Grammar of



ggpubr
y
ggrepel
y
ggsci
y
ggsignif
y
gifski
y
glmnet
y

gplots

GNU R package “Various R Programming Tools for Plotting



gridSVG
y

gtable

GNU R package “Arrange grobs in tables.”



gtools

GNU R package “Various R Programming Tools”



haven
y
igraph
y
interactions
y
jpeg
y

labeling

GNU R package “Axis Labeling”



lambda.r

GNU R package “Modeling Data with Functional Programming”



lattice

GNU R package “Lattice Graphics”



latticeExtra
y
leaps

GNU R package “regression subset selection”

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

GNU R package for linear mixed effects model fitting

y
locfit
y
lubridate
y

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.db


mixdist
y
modelr
y
multcomp
y

munsell

GNU R package “Munsell colour system”



mvtnorm
y
network
y

nlme

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



nloptr
y
ontologyIndex
y

optparse

GNU R package “Command line option parser.”



permute

GNU R package “Functions for Generating Restricted



pheatmap
y
pbkrtest
y
plotly
y
plotROC
y
plotrix

GNU R package “Various plotting functions”

y

plyr

GNU R package “Tools for Splitting, Applying and Combining



polynom
y

proto

GNU R package “Prototype object-based programming”

y
quantmod
y
quantreg
y

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

y

reshape2

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

y
reticulate
y

rggobi

GNU R package for the GGobi data visualization system

y

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

y
RMySQL
y
ROCR
y

rserve

GNU R Rserve tcp/ip server and sample clients

y
rstatix
y

rsqlite

GNU R package “SQLite Interface for R”



rvest
y

scales

GNU R package “Scale Functions for Visualization”



scatterplot3d

GNU R package “3D Scatter Plot”

y
servr
y
Seurat
y
shape
y
shiny
y
shinyjs
y
sna
y

sp

GNU R package “Classes and Methods for Spatial Data”



sqldf
y
statnet.common
y

stringr

GNU R package “Simple, Consistent Wrappers for Common



tcltk2

GNU R package “Tcl/Tk Additions”

y

testthat

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



tibble
y
tidyr
y
tidyverse
y
transformr
y

vegan

GNU R package “Community Ecology Package”



VennDiagram
y
VGAM
y
vioplot
y
xfun
y

xml

GNU R package “Tools for Parsing and Generating XML Within

y

xtable

GNU R coerce data to LaTeX and HTML tables



Additional R BioConductor Tools (cqbhiera/common.yaml) how to differentiate BioConductor tools

SoftwareDescription
affy
y
affyio

GNU R package “Tools for parsing Affymetrix data files”


annotate

GNU R package “Annotation for microarrays”


annotationdbi

GNU R package “Annotation Database Interface”


arrayQualityMetrics
y
ballgownFlexible, isoform-level differential expression analysisy
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 searchingy
BSgenome.Hsapiens.UCSC.hg19
y
ChIPseekerannotating ChIP-seq data analysisy
cummeRbundanalyzing Cufflinks RNA-Seq outputy
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 distributiony
devtools

Collection of package development tools

y
DEXSeqfinding differential exon usage using RNA-seq exon counts between samplesy
genfilter

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


ggplot2movies

GISPA
y
GOstatstools for interacting with GO and microarray datay
GO.db
y

hilbertvis

GNU R package to visualise long vector data


httpuv
y

iranges

GNU R package “Infrastructure for manipulating intervals


JunctionSeq
y

limma

GNU R package “Linear Models for Microarray Data”


mirbase.db
y

multtest

GNU R package “Resampling-based multiple hypothesis


org.Hs.eg.db
y
org.Sc.sgd.db
y
org.Mm.eg.db
y
org.Rn.eg.db
y

preprocesscore

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


processx
y
pkgload
y
qvalue

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


rhdf5

provides an interface between HDF5 and R

y
readr
y
ReportingTools
y
RIPSeekeridentify protein-associated transcripts from RIP-seq experimentsy
roxygen2
y
rsamtools

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


s4vectors

GNU R package “S4 implementation of vectors and lists”


SISPA
y
sleuthanalysis of RNA-Seq experiments for which transcript abundances have been quantified with kallistoy
ShortReadsampling, iteration, and input of FASTQ filesy
topGO
y
TxDb.Scerevisiae.UCSC.sacCer3.sgdGene
y
TxDb.Hsapiens.UCSC.hg38.knownGene
y
tximport
y
WGCNA
y

xvector

GNU R package “Representation and manpulation of external


yardstick
y

zlibbioc

GNU R package “An R packaged zlib-1.2.5″


Additional Perl CPAN modules (cqbprofile/manifest/perl.pp and cqb-maker)

SoftwareDescriptionin perl.pp or cqb-maker?
Bit::Vector
y
CGI
y
DBI
y
DBD::SQLite
y
File::Which
y
forks
y
forks::shared
y
Graph
y
IO::All
y
IO:Prompt
y
LWP
y
Math::Cephes
y
Module::Build
y
Net::HTTP
y
Perl::Unsafe::Signals
y
Statistics::Descriptive
y
Switch
y
Test::Class
y
Test::More
y
Test::Exception
y
Test::Harness
y
XML::Simple
y

Next Generation Sequencing (NGS) Tools (cqbprofile/manifest/next_gen_sequencing_client.pp)

SoftwareDescriptionPathin next_gen_sequencing_client.pp
bamtoolsSAM/BAM file manipulation/stor/system/opt/gitdir/bamtools/bin/bamtoolsy
bcl2fastqBCL file manipulation/usr/bin/bcl2fastqy
deeptools

y
enabrowsertools

y
hisat

y
fastq_screen


guppy

y
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
y

bedtools

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

y
scalangs

y
sra toolkitSRA file manipulation/stor/system/opt/sratoolkit.2.7.0-ubuntu64y
stringtie

y
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 (cqbprofile/manifest/rna_sequencing_client.pp)

SoftwareDescriptionPathin rna_sequencing_client.pp
augustus

y
busco

y
cellranger

y
cufflinks

y
expressExpression quantification/usr/bin/expressy
fastqc

y
featurecountsCounting/usr/bin/featureCountsy
htseqCounting/stor/system/opt/HTSeq-0.6.1p1y
kallistoExpression quantification/usr/bin/kallistoy
STARAlignment/usr/bin/STAR
/usr/bin/STARlong
y
tophat

y
MultiQCReport Generation/usr/bin/multiqcy
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/rnaseqcy
salmon

y
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/

Specialized NGS Tools (specialized_sequencing_client.pp)

SoftwareDescriptionPathin specialized_sequencing_client.pp
BWA

y
bwa_mem2

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

y
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/y
artnext generation sequencing read simulator/usr/bin/art_454
/usr/bin/art_illumina
/usr/bin/art_SOLiD
y

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.

SoftwareDescriptionPathin variant_analysis_client.pp
annovarAnnotation of variants/stor/system/opt/annovar/y
gatkHuman/higher-vertabrate variant detection toolkit/stor/system/opt/gatk-3.6/y
MuTectSomatic Mutations/stor/system/opt/gatk-3.6/
/stor/system/opt/mutect/
y
plink

GWAS tools

/usr/bin/plinky
snpeffGenetic variant annotation and effect prediction/stor/system/opt/snpEffy

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.

SoftwareDescriptionPathin genome_client.pp
consedcontig assembly tools/usr/local/genome/consed/y
phrapcontig assembly tools/usr/local/genome/bin/y
phredcontig assembly tools/usr/local/genome/bin/y
glimmermicobial gene annotations/usr/bin/glimmer2
/usr/bin/build-icm
/usr/bin/extract
/usr/bin/long-orfs
y

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
docker
Marcotte 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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