POD Software Information

Overview

All POD compute servers have identical Ubuntu 19.04 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.

Standard OS Software

Software	Description
build-essential	gcc, g++, make, cmake, patch, autoconf, automake, m4, bison, libtool
emacs, vi, vim, ed	text editors
postfix	mail programs
perl	perl interpretor
python 2	python version 2 interpretor
python 3	python version 3 interpretor
ruby	ruby programming language
samba	Windows SMB/CIFS file and printer sharing protocol and applications
screen, tmux	Text window managers (multiplexer)
ssh	Secure Shell (remote access)
sudo	Root access for POD delegates only
tar	File archiving utility
wget, curl	Remote file/url transfer utilities
gzip, zip, unzip	File compression and archiving tools.

Standard Third-Party Software

Software	Description
R, Rscript	R command-line shell and script execution programs.
Matlab	MathWorks Matlab Software. See How do I use MATLAB on the POD?

Additional Development Tools

Software	Description
scons	Software build tool
swig	Software development tool
sqlite3	SQL Lite databases
git	Version control utilities

Additional Python Tools

Software	Description
blaze	An interface to query data on different storage systems
cutadapt	Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads
dendropy	phylogenetic computing
leukgen-disambiguate
MACS2	Model Based Analysis for ChIP-Seq data
maplot
matplotlib	python 2D plotting library
networkx	Creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
nimfa	Nonnegative matrix factorization
numpy	scientific computing with Python
pandas	Python Data Analysis Library
patsy
pip	Python installation program (to install python modules)
plotly
pysam
pyvttbl
reportlab
rpy2	Python interface to R
seaborn
scipy	Collection of Python software for mathematics, science, and engineering.
sklearn	Machine Learning in Python
skimage	Image processing in Python
statsmodels	Estimation of statistical models

Additional R Tools

Software	Description
abind
cargo
cowplot
curl
foreach
gganimate
GGally
ggpubr
ggrepel
gifski
gridSVG
igraph
jpeg
leaps
lme4
lubridate
mirbase.db
mixdist
multcomp
mvtnorm
network
pheatmap
plotly
plotROC
plotrix
quantmod
RMySQL
sna
sqldf
tidyr
VGAM
vioplot

Additional R BioConductor Tools

Software	Description
affy
arrayQualityMetrics
ballgown	Flexible, isoform-level differential expression analysis
BSgenome	Efficient genome searching
BSgenome.Hsapiens.UCSC.hg19
ChIPseeker	annotating ChIP-seq data analysis
cummeRbund	analyzing Cufflinks RNA-Seq output
DESeq2	Estimate 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
DEXSeq	finding differential exon usage using RNA-seq exon counts between samples
GISPA
GOstats	tools for interacting with GO and microarray data
GO.db
JunctionSeq
mirbase.db
org.Sc.sgd.db
org.Mm.eg.db
rhdf5	provides an interface between HDF5 and R
readr
ReportingTools
rhdf5
RIPSeeker	identify protein-associated transcripts from RIP-seq experiments
SISPA
sleuth	analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto
ShortRead	sampling, iteration, and input of FASTQ files
topGO
TxDb.Scerevisiae.UCSC.sacCer3.sgdGene
TxDb.Hsapiens.UCSC.hg38.knownGene
tximport
WGCNA

Additional Perl CPAN modules

Software	Description
CGI
DBI
Graph
LWP
Math::Cephes
Net::HTTP
Statistics::Descriptive
Switch
Test::Class
Test::More
Test::Exception
Test::Harness
XML::Simple

Next Generation Sequencing (NGS) Tools

Software	Description	Path
bamtools	SAM/BAM file manipulation	/stor/system/opt/gitdir/bamtools/bin/bamtools
bcl2fastq	BCL file manipulation	/usr/bin/bcl2fastq
samtools	SAM/BAM file manipulation	/usr/bin/samtools /usr/bin/samtools_0.1.18 /usr/bin/samtools-1.3
picard	SAM/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
sra toolkit	SRA file manipulation	/stor/system/opt/sratoolkit.2.7.0-ubuntu64
bwa	Alignment	/usr/bin/bwa /usr/bin/bwa-0.5.9 /usr/bin/bwa5 /usr/bin/bwa-0.6.2 /usr/bin/bwa6

RNA Sequencing Tools

Software	Description	Path
express	Expression quantification	/usr/bin/express
featurecounts	Counting	/usr/bin/featureCounts
htseq	Counting	/stor/system/opt/HTSeq-0.6.1p1
kallisto	Expression quantification	/usr/bin/kallisto
STAR	Alignment	/usr/bin/STAR /usr/bin/STARlong
MultiQC	Report Generation	/usr/bin/multiqc
RNA-SeQC	QC 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
hisat	Spliced alignment for mapping RNA-seq reads	/stor/system/opt/hisat-0.1.6-beta
hisat2	Align NGS reads (both DNA and RNA) against a reference genome	/stor/system/opt/hisat2-2.0.5/

Specialized NGS Tools

Software	Description	Path
MultiQC	Report Generation	/usr/bin/multiqc
eisen cluster	hierachical & k-means clustering	/usr/bin/cluster-eisen
meme suite	motif analysis	/stor/system/opt/meme_4.11.2
meme_chip	motif analysis suite for ChIP-seq	/stor/system/opt/software/meme-chip/4.11.2/
art	next generation sequencing read simulator	/usr/bin/art_454 /usr/bin/art_illumina /usr/bin/art_SOLiD

Variant Analysis Tools

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

Software	Description	Path
annovar	Annotation of variants	/stor/system/opt/annovar/
gatk	Human/higher-vertabrate variant detection toolkit	/stor/system/opt/gatk-3.6/
MuTect	Somatic Mutations	/stor/system/opt/gatk-3.6/ /stor/system/opt/mutect/
plink	GWAS tools	/usr/bin/plink
snpeff	Genetic variant annotation and effect prediction	/stor/system/opt/snpEff

Evolutionary Analysis Tools

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

Software	Description	Path
mauve

Genome/Transcriptome Assembly Tools