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All POD compute servers have (nearly) identical Ubuntu 1820.04 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 And some PODs also have additional software installed which that is unique to that POD.Let us know if there is additional software you would like to have installed.

Installing software

Users can perform local (per-user) installations that do not require administrative (root/sudo) access. For software that does require sudo, or if you would like a package installed globally for use by others, please email us at rctf-support@utexas.edu.

Programs in /stor/system/opt

Some tool "suites" that have many sub-program binaries, are not made 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. Examples include multiple versions of the sratoolkit and the picard-tools suites. E.g.:

Code Block
languagebash
export PATH="/stor/system/opt/sratoolkit.2.8.2-ubuntu64/bin:$PATH"

Programs in /mnt/bioi/tools

All compute servers have a shared, read-only /mnt/bioi directory mounted that contains many useful bioinformatics resources such as annotations and other references in /mnt/bioi/ref_genome and external data in /mnt/bio/data).T

Specifically, the /mnt/bioi/tools directory contains several tool suites and their associated data (e.g. cellranger, GSEA), and each tool suite directory has multiple tool version sub-directories. Like the suites in /stor/system/opt, the associated binaries are not on your PATH by default, but can be added as needed, e.g.:

Code Block
languagebash
export PATH="/mnt/bioi/tools/cellranger/8.0.0/bin":$PATH
export PATH="/mnt/bioi/tools/UCSC_utils/2023_08:$PATH"

Multiple software versions

Unlike TACC, we do not implement a module system. Rather, we install different versions of a program side-by-side, with names differing by their versions (for example:

  • Rscript (the default version, same as Rscript-4-3.1), Rscript-4.3.1, Rscript-4.0.3, Rscript-3.6.3
  • samtools (the default, version 1.10), samtools-1.9, samtools-1.11

In particular, multiple versions of R and Python are installed side-by-side. For more information, see:

Often you can see if there are multiple versions of a program installed just by typing its name and hitting the Tab key twice. For example, typing bedtools then Tab Tab shows this:

Code Block
bedtools         bedtools-2.25.0  bedtools-2.26.0  bedtools-2.27.1  bedtools-2.28.0

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 and About Python and JupyterHub server help pages.

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 InterfaceWeb Interface

After the August 2023 maintenance, all POD compute servers now use R 4.3.1 as the R version in their RStudio Server web application. If your POD has multiple compute servers and you would like one to run a different R version, please contact us at rctf-support@utexas.edu.

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
in cqb-biolinux?y
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

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

bwa0.7.17-1ubuntu0.1

Burrows-Wheeler Aligner

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-Seqcufflinks

2.2.1+dfsg.1-2

Transcript assembly, differential expression and regulation for RNA-Seq

diamond2.0.14sequence aligner for protein and translated DNA searches
DiffBind3.0.15Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data

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

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

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

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

minfi1.24.0

Analyze Illumina Infinium DNA methylation arrays

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

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

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

yRsubread2.4.3

Mapping, quantification and variant analysis of sequencing data

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

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

tophat

2.1.1+dfsg1-1

fast splice junction mapper for RNA-Seq reads

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?

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)
y
SoftwarePython2 VersionPython3 VersionDescription

in devel_tools

all-devy


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 Python
skimage

Image processing in Pythony
statsmodels0.8.00.8.0Estimation of statistical modelsy
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

...

)
yyy
SoftwareDescription

in common.yaml

listed in library()
abind

GNU R package “Combine multi-dimensional arrays”

y

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,

y

y
carCompanion to Applied Regressionyy
cargoy

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

Streamlined Plot Theme and Plot Annotations for 'ggplot2'

yy
curlA Modern and Flexible Web Client for Ryy

data.table

GNU R package “Extension of data.frame”

y

dbi

GNU R package “R Database Interface”

dbplyrR Database Interfaceyy
dendextendExtending 'dendrogram' Functionality in Ry

dichromat

Color schemes for dichromats

y

digest

GNU R package “Create Cryptographic Hash Digests of R

y

emmeans

Estimated Marginal Means, aka Least-Squares Means

y

y

evaluate

GNU R package “Parsing and Evaluation Tools that Provide

y

fivethirtyeight

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

yy

'

forcats

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

y

y
foreachProvides Foreach Looping Constructyy

futile.logger

GNU R package “A Logging Utility for R”

y

futile.options

GNU R package “Futile options management”

y

gdata

GNU R package “Various R Programming Tools for Data

y

getopt

GNU R package “C-like getopt behavior.”

gganimateA Grammar of Animated Graphicsyy
GGallyExtension to 'ggplot2'yy
ggExtra

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

y

y

ggplot2

GNU R package “An Implementation of the Grammar of

y
ggpubr'ggplot2' Based Publication Ready Plotsyy
ggrepel

Automatically Position Non-Overlapping Text Labels with 'ggplot2'

yy

ggsci

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

yy
ggsignifSignificance Brackets for 'ggplot2'yy
gifskiHighest Quality GIF Encoderyy
glmnet

Lasso and Elastic-Net Regularized Generalized Linear Models

yy

gplots

GNU R package “Various R Programming Tools for Plotting

y
gridSVGExport 'grid' Graphics as SVGy
ygtBuild display tables from tabular data with an easy-to-use set of functions

gtable

GNU R package “Arrange grobs in tables.”

y

gtools

GNU R package “Various R Programming Tools”

y

haven

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

yy

Files

igraphNetwork Analysis and Visualizationyy
interactions

Comprehensive, User-Friendly Toolkit for Probing Interactions

yy
jpegRead and write JPEG imagesyy

labeling

GNU R package “Axis Labeling”

y

lambda.r

GNU R package “Modeling Data with Functional Programming”

y

lattice

GNU R package “Lattice Graphics”

y
latticeExtraExtra Graphical Utilities Based on Latticeyy
leaps

GNU R package “regression subset selection”

y

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

yy
locfit

Local Regression, Likelihood and Density Estimation

yy
lubridateMake Dealing with Dates a Little Easieryy

matrix

GNU R package of classes for dense and sparse matrices

y

matrixstats

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

y

mirbase.dbmiRBase: the microRNA databasey
mixdistFinite Mixture Distribution Modelsyy
modelr

Modelling Functions that Work with the Pipe

yy

multcomp

Simultaneous Inference in General Parametric Models

y

y

munsell

GNU R package “Munsell colour system”

y

mvtnormMultivariate Normal and t Distributionsyy
networkClasses for Relational Datayy

nlme

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

y

nloptrR Interface to NLoptyy
ontologyIndexFunctions for Reading Ontologies into Ryy

optparse

GNU R package “Command line option parser.”

permute

GNU R package “Functions for Generating Restricted

pheatmapPretty Heatmapsyy
pbkrtest

Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison

yy

plotlyCreate Interactive Web Graphics via 'plotly.js'yy
plotROC

Generate Useful ROC Curve Charts for Print and Interactive Use

yy

plotrix

GNU R package “Various plotting functions”

yy

plyr

GNU R package “Tools for Splitting, Applying and Combining

y
polynom

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

yy

proto

GNU R package “Prototype object-based programming”

yy

quantmodQuantitative Financial Modelling Frameworkyy
quantregQuantile Regressionyy

r.methodss3

GNU R package “Utility function for defining S3 methods”

y

rcolorbrewer

GNU R package providing suitable color palettes

y

rcpp

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

y

rcurl

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

y

relimp

GNU R package “Relative Contribution of Effects in a

y

reshape2

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

y

y
reticulateInterface to 'Python'yy

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

RMySQLDatabase Interface and 'MySQL' Driver for Ryy
ROCR

Visualizing the Performance of Scoring Classifiers

y

y

rserve

GNU R Rserve tcp/ip server and sample clients

y

rstatix

Pipe-Friendly Framework for Basic Statistical Tests

yy

rsqlite

GNU R package “SQLite Interface for R”

y

rvestEasily Harvest (Scrape) Web Pagesyy

scales

GNU R package “Scale Functions for Visualization”

y

scatterplot3d

GNU R package “3D Scatter Plot”

yy
servr

A Simple HTTP Server to Serve Static Files or Dynamic Documents

yy

SeuratTools for Single Cell Genomicsyy
shapeFunctions for Plotting Graphical Shapes, Colorsyy
shinyWeb Application Framework for Ryy
shinyjs

Easily Improve the User Experience of Your Shiny Apps in Seconds

y
yshowtextMaking 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 datay
snaTools for Social Network Analysisyy

sp

GNU R package “Classes and Methods for Spatial Data”

sqldfManipulate R Data Frames Using SQLyy
statnet.common

Common R Scripts and Utilities Used by the Statnet Project Software

yy

stringr

GNU R package “Simple, Consistent Wrappers for Common

y

Common

sysfontsLoading system fonts and Google Fonts into R

tcltk2

GNU R package “Tcl/Tk Additions”

yy

testthat

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

y
tibbleSimple Data Framesyy
tidyrTidy Messy Datay
tidyverseEasily Install and Load the 'Tidyverse'yy
transformrPolygon and Path Transformationsyy

vegan

GNU R package “Community Ecology Package”

VennDiagramGenerate High-Resolution Venn and Euler Plotsyy
VGAMVector Generalized Linear and Additive Modelsyy
vioplotViolin Ploty
xfunMiscellaneous Functions by 'Yihui Xie'yy

xml

GNU R package “Tools for Parsing and Generating XML Within

yy

xtable

GNU R coerce data to LaTeX and HTML tables

y

Additional R BioConductor Tools

(in repo cqbhiera/common.yaml)

...

in common.yaml
SoftwareDescriptionin library()
affyMethods for Affymetrix Oligonucleotide Arraysyy
affyio

GNU R package “Tools for parsing Affymetrix data files”

y
annotate

GNU R package “Annotation for microarrays”

y

annotationdbi

GNU R package “Annotation Database Interface”

y
arrayQualityMetricsQuality metrics report for microarray data setsyy
ballgownFlexible, isoform-level differential expression analysisyyanalysis
biobase

GNU R package “Biobase: Base functions for Bioconductor”

y

biocgenerics

GNU R package “S4 generic functions for Bioconductor”

y

biocinstaller

GNU R package “Install/Update Bioconductor and CRAN

biocparallel

GNU R package “Bioconductor facilities for parallel

y

biomart

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

y

biostrings

GNU R package “String objects representing biological

y
BSgenomeEfficient genome searchingyy
BSgenome.Hsapiens.UCSC.hg19

Full genome sequences for Homo sapiens (UCSC version hg19)

yy

ChIPseekerannotating ChIP-seq data analysisyy
cummeRbundanalyzing Cufflinks RNA-Seq outputyy
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 distributionyy
devtools

Collection of package development tools

yy

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

GNU R package “genefilter: methods for filtering genes

y

geneplotter

Graphics related functions for Bioconductor

y

genomeinfodb

GNU R package “Utilities for manipulating chromosome and

y

genomicalignments

GNU R package “Representation and manipulation of short

y

genomicranges

GNU R package “Representation and manipulation of genomic

y
ggplot2moviesMovies Datay
GISPA

GISPA: Method for Gene Integrated Set Profile Analysis

yy

GOstatstools for interacting with GO and microarray datayy
GO.dby

hilbertvis

GNU R package to visualise long vector data

httpuvHTTP and WebSocket Server Libraryyy

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

yy

limma

GNU R package “Linear Models for Microarray Data”

y

mirbase.dbmiRBase: the microRNA databaseyy

multtest

GNU R package “Resampling-based multiple hypothesis

org.Hs.eg.dbGenome wide annotation for Humanyy
org.Sc.sgd.dbGenome wide annotation for Yeastyy
org.Mm.eg.dbGenome wide annotation for Mouseyy
org.Rn.eg.dbGenome wide annotation for Ratyy

preprocesscore

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

y
processxExecute and Control System Processesyy
pkgloady
qvalue

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

y

rhdf5

provides an interface between HDF5 and R

yy

readrRead Rectangular Text Datayy
ReportingToolsTools for making reports in various formatsyy
RIPSeekeridentify protein-associated transcripts from RIP-seq experimentsyy
roxygen2In-Line Documentation for Ryy
rsamtools

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

y

s4vectors

GNU R package “S4 implementation of vectors and lists”

y

SISPA

SISPA: Method for Sample Integrated Set Profile Analysis

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

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

yy

WGCNAWeighted Correlation Network Analysisyy

xvector

GNU R package “Representation and manpulation of external

y

yardstickTidy Characterizations of Model PerformanceyyPerformance

zlibbioc

GNU R package “An R packaged zlib-1.2.5″

y

Additional Perl CPAN modules

(in repo cqbprofile/manifest/perl.pp and cqb-maker)
y
SoftwareDescriptionin perl.pp or cqb-maker?
Bit::Vectory
CGIy
DBI
DBD::SQLitey
File::Whichy
forksy
forks::sharedy
Graphy
IO::Ally
IO:Prompty
LWPy
Math::Cephesy
Module::Buildy
Net::HTTPy
Perl::Unsafe::Signalsy
Statistics::Descriptivey
Switchy
Test::Classy
Test::Morey
Test::Exceptiony
Test::Harnessy
XML::Simpley

Next Generation Sequencing (NGS) Tools

(in repo 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
deeptoolsy

enabrowsertoolsy

hisaty

fastq_screen

guppyy

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-2.5.0y

bedtools

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

scalangsy

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

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)
SoftwareDescriptionPathin rna_sequencing_client.pp
augustusyprogram to find genes and their structures in one or more genomes
buscoy

cellrangery

cufflinksy

expressExpression quantification/usr/bin/expressy
fastqcy

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
tophaty

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
salmony

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

y

Specialized NGS Tools

(in repo specialized_sequencing_client.pp)
SoftwareDescriptionPathin specialized_sequencing_client.pp
BWAy

bwa_mem2y

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

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 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
ISEScanidentification of insertion sequence elements in genomes/usr/lib/libssw.soy
FragGeneScanrequirement of ISEScan/usr/bin/FragGeneScan1.30y

Molecular Structures Client

mgltools
SoftwareDescriptionPathin molecular_structures_client.pp
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

...

SoftwareDescriptionLocationPath
bam2fastq
Iyer POD/stor/system/opt/bam2fastq-1.1.0/
basespace
GSAF POD
canu
Chen POD
crossstitch
Ochman PODdockerMarcotte 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

...