POD Software Information

All POD compute servers have identical BioLinux 8 Operating System configurations, which is based Ubuntu 14.04 LTS, plus a number of additional packages we have identified.

Some PODs 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
mail, mailx, 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
whois	Whois directory client.
gzip, zip, unzip	File compression and archiving tools.

Standard Third-Party Software

Software	Description
R, R Studio	R and R studio statistical package
Matlab	MathWorks Matlab Software

Additional Development Tools

Software	Description
scons	Software build tool
swig	Software development tool
sqlite3	SQL Lite databases
git, svn, cvs, mercurial	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
MACS2	Model Based Analysis for ChIP-Seq data
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
pip	Python installation program (to install python modules)
rpy2	Python interface to R
scipy	Collection of Python software for mathematics, science, and engineering.
sklearn	Machine Learning in Python
skimage	Image processing in Python

Additional R Tools

Software	Description
curl
igraph
jpeg
lubridate
mirbase.db
mixdist
network
quantmod
RMySQL
sna
sqldf
tidyr
VGAM
vioplot

Additional R BioConductor Tools

Software	Description
BSgenome	Efficient genome searching
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
GOstats	tools for interacting with GO and microarray data
GO.db
mirbase.db
org.Sc.sgd.db
org.Mm.eg.db
rhdf5
RIPSeeker
ShortRead
sleuth
TxDb.Scerevisiae.UCSC.sacCer3.sgdGene
TxDb.Hsapiens.UCSC.hg38.knownGene
BSgenome.Hsapiens.UCSC.hg19
ballgown

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/
hisat	spliced alignment for mapping RNA-seq reads
hisat2	align NGS reads (both DNA and RNA) against a genome population

Specialized Sequencing Tools

Software	Description	Path
bwa	Alignment	/usr/bin/bwa /usr/bin/bwa-0.5.9 /usr/bin/bwa5 /usr/bin/bwa-0.6.2 /usr/bin/bwa6
eisen cluster	hierachical & k-means clustering	/usr/bin/cluster-eisen
meme_chip	motif analysis toolkit suite	/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

RNA Sequencing Tools

Software	Description	Path
express	Expression quantification	/usr/bin/express
featurecounts	Counting	/usr/bin/featureCounts
htseq	Counting	(perl 2.7)
kallisto	Expression quantification	/usr/bin/kallisto
STAR	Alignment	/usr/bin/STAR /usr/bin/STARlong

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

Evolution Sequencing Tools

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

Software	Description	Path
mauve
orthomcl	NOT YET IMPLEMENTED

Genome/Transcriptome Assembly Tools