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
R, R Studio	R and R student statistical package
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.

Additional Development Tools

Software	Description
scons
swig
sqlite3	SQL Lite databases
git, svn, cvs, mercurial	Version control utilities

Additional Python Tools

Software	Description
blaze
cutadapt
dendropy
MACS2
matplotlib
networkx
nimfa
numpy
pandas
pip
rpy2
scipy
sklearn
skimage

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
ChIPseeker
cummeRbund
DESeq2
devtools
DEXSeq
GOstats
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

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
bamtools	SAM/BAM file manipulation
bcl2fastq	BCL file manipulation
samtools	SAM/BAM file manipulation
picard	SAM/BAM file manipulation
bedtools	BED/GFF file manipulation
sra toolkit	SRA file manipulation

Specialized Sequencing Tools

Software	Description
bwa	Alignment
eisen cluster	hierachical & k-means clustering
meme_chip	motif analysis toolkit suite
art	next generation sequencing read simulator

RNA Sequencing Tools

Software	Description
express	Expression quantification
featurecounts	Counting
htseq	Counting
kallisto	Expression quantification
STAR	Alignment

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
annovar	Annotation of variants
gatk	Human/higher-vertabrate variant detection toolkit
MuTect	Somatic Mutations
plink	GWAS tools
snpeff	Genetic variant annotation and effect prediction

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
mauve
orthomcl	NOT YET IMPLEMENTED

Genome/Transcriptome Assembly Tools