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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, unzip

File compression and archiving tools.

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

Standard BioLinux Packages

(how to 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


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-Seq


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

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

y

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?

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
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

(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
y

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 R
y

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

yy

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'

yy
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

yy

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 SVGyy

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
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”

yy
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 database
y
mixdistFinite Mixture Distribution Modelsyy
modelr

Modelling Functions that Work with the Pipe

yy
multcomp

Simultaneous Inference in General Parametric Models

yy

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

yy
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

yy

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

yy
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

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 Datayy
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 Plotyy
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

(cqbhiera/common.yaml) how to differentiate BioConductor tools
SoftwareDescriptionin common.yamlin 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 analysisyy
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 Data
y
GISPA

GISPA: Method for Gene Integrated Set Profile Analysis

yy
GOstatstools for interacting with GO and microarray datayy
GO.db
y

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
pkgload
y
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 Performanceyy

zlibbioc

GNU R package “An R packaged zlib-1.2.5″


y

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/
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

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

Molecular Structures Client

SoftwareDescriptionPathin molecular_structures_client.pp
mgltools



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
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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