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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.

Standard OS Software

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, unzipFile compression and archiving tools.

Standard BioLinux Packages

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

bedtools

2.26.0+dfsg-5

suite of utilities for comparing genomic features

bioperl

1.7.2-2

Perl tools for computational molecular biology

bioperl-run

1.7.1-3

BioPerl wrappers: scripts

blast2

1:2.6.0-1

Basic Local Alignment Search Tool

bowtie

1.2.2+dfsg-2

Ultrafast memory-efficient short read aligner

bowtie2

2.3.4.1-1

Ultrafast memory-efficient short read aligner

bwa

0.7.17-1

Burrows-Wheeler Aligner

cd-hit

4.6.8-1

a suite of programs designed to quickly group sequences

clustalw

2.1+lgpl-5

No description

clustalx

2.1+lgpl-6

No description

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

emboss

6.6.0+dfsg-6build1

european molecular biology open software suite

emboss-lib

6.6.0+dfsg-6build1

EMBOSS Libraries

fastdnaml

1.2.2-12

Tool for construction of phylogenetic trees of DNA sequences

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

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

jellyfish

2.2.8-3build1

count k-mers in DNA sequences

khmer

2.1.2+dfsg-3

k-mer counting, filtering and graph traversal

libbiojava-java

1:1.7.1-7

Java API to biological data and applications (default version)

libbiojava-java-demos

1:1.7.1-7

Example programs for BioJava

macs

2.1.1.20160309-2

Model-based Analysis of ChIP-Seq on short reads sequencers

mafft

7.310-1

Multiple alignment program for amino acid or nucleotide sequences

maq

0.7.1-7

maps short fixed-length polymorphic DNA sequence reads to reference sequences

microbiomeutil

20101212+dfsg1-1build1

Microbiome Analysis Utilities

mothur

1.39.5-2build1

sequence analysis suite for research on microbiota

mothur-mpi

1.39.5-2build1

mpi-enabled binary for mothur

mrbayes-mpi

3.2.6+dfsg-2

Bayesian Inference of Phylogeny – mpi version

mummer

3.23+dfsg-3

Efficient sequence alignment of full genomes

muscle

1:3.8.31+dfsg-3

Multiple alignment program of protein sequences

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

ncbi-tools-bin

6.1.20170106-2

NCBI libraries for biology applications (text-based utilities)

ncbi-tools-x11

6.1.20170106-2

NCBI libraries for biology applications (X-based utilities)

paml

4.9g+dfsg-3

Phylogenetic Analysis by Maximum Likelihood (PAML)

parafly

0.0.2013.01.21-3build1

parallel command processing using OpenMP

phylip

1:3.696+dfsg-5

No description

phyml

3:3.3.20170530+dfsg-2

Phylogenetic estimation using Maximum Likelihood

picard-tools

2.8.1+dfsg-3

Command line tools to manipulate SAM and BAM files

primer3

2.4.0-1ubuntu2

Tool to design flanking oligo nucleotides for DNA amplification

pymol

1.8.4.0+dfsg-1build1

Molecular Graphics System

qiime

3:3.3.20170530+dfsg-2

Quantitative Insights Into Microbial Ecology

















Standard Third-Party Software

SoftwareDescription
R, RscriptR command-line shell and script execution programs.
MatlabMathWorks Matlab Software.
See How do I use MATLAB on the POD?

Additional Development Tools

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

Additional Python Tools

SoftwareDescription
blazeAn interface to query data on different storage systems
cutadaptFinds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads
dendropyphylogenetic computing
leukgen-disambiguate
MACS2

Model Based Analysis for ChIP-Seq data

maplot
matplotlibpython 2D plotting library
networkxCreation, manipulation, and study of the structure, dynamics, and functions of complex networks.
nimfaNonnegative matrix factorization
numpyscientific computing with Python
pandasPython Data Analysis Library
patsy
pipPython installation program (to install python modules)
plotly
pysam
pyvttbl
reportlab
rpy2Python interface to R
seaborn
scipyCollection of Python software for mathematics, science, and engineering.
sklearnMachine Learning in Python
skimageImage processing in Python
statsmodelsEstimation of statistical models


Additional R Tools

SoftwareDescription
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

SoftwareDescription
affy
affyio

GNU R package “Tools for parsing Affymetrix data files”

annotate

GNU R package “Annotation for microarrays”

annotationdbi

GNU R package “Annotation Database Interface”

arrayQualityMetrics
ballgownFlexible, isoform-level differential expression analysis
biobase

GNU R package “Biobase: Base functions for Bioconductor”

biocgenerics

GNU R package “S4 generic functions for Bioconductor”

biocinstaller

GNU R package “Install/Update Bioconductor and CRAN

biocparallel

GNU R package “Bioconductor facilities for parallel

biomart

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

biostrings

GNU R package “String objects representing biological

BSgenomeEfficient genome searching
BSgenome.Hsapiens.UCSC.hg19
ChIPseekerannotating ChIP-seq data analysis
cummeRbundanalyzing Cufflinks RNA-Seq output
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 distribution
devtools

Collection of package development tools

DEXSeqfinding differential exon usage using RNA-seq exon counts between samples
genfilter

GNU R package “genefilter: methods for filtering genes

geneplotter

Graphics related functions for Bioconductor

genomeinfodb

GNU R package “Utilities for manipulating chromosome and

genomicalignments

GNU R package “Representation and manipulation of short

genomicranges

GNU R package “Representation and manipulation of genomic

GISPA
GOstatstools for interacting with GO and microarray data
GO.db

hilbertvis

GNU R package to visualise long vector data

iranges

GNU R package “Infrastructure for manipulating intervals

JunctionSeq

limma

GNU R package “Linear Models for Microarray Data”

mirbase.db

multtest

GNU R package “Resampling-based multiple hypothesis

org.Sc.sgd.db
org.Mm.eg.db

preprocesscore

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

qvalue

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

rhdf5

provides an interface between HDF5 and R

readr
ReportingTools
RIPSeekeridentify protein-associated transcripts from RIP-seq experiments
rsamtools

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

s4vectors

GNU R package “S4 implementation of vectors and lists”

SISPA
sleuthanalysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto
ShortReadsampling, iteration, and input of FASTQ files
topGO
TxDb.Scerevisiae.UCSC.sacCer3.sgdGene
TxDb.Hsapiens.UCSC.hg38.knownGene
tximport
WGCNA

xvector

GNU R package “Representation and manpulation of external

zlibbioc

GNU R package “An R packaged zlib-1.2.5″

Additional Perl CPAN modules

SoftwareDescription
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

SoftwareDescriptionPath
bamtoolsSAM/BAM file manipulation/stor/system/opt/gitdir/bamtools/bin/bamtools
bcl2fastqBCL file manipulation/usr/bin/bcl2fastq
hisat

fastq_screen

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

bedtools

BED/GFF file manipulation/usr/bin/bedtools-2.17.0
/usr/bin/bedtools-2.25.0
sra toolkitSRA file manipulation/stor/system/opt/sratoolkit.2.7.0-ubuntu64
stringtie

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

SoftwareDescriptionPath
augustus

busco

cufflinks

expressExpression quantification/usr/bin/express
fastqc

featurecountsCounting/usr/bin/featureCounts
htseqCounting/stor/system/opt/HTSeq-0.6.1p1
kallistoExpression quantification/usr/bin/kallisto
STARAlignment/usr/bin/STAR
/usr/bin/STARlong
tophat

MultiQCReport Generation/usr/bin/multiqc
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/rnaseqc
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/

Specialized NGS Tools

SoftwareDescriptionPath
BWA

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

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/
artnext 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.

SoftwareDescriptionPath
annovarAnnotation of variants/stor/system/opt/annovar/
gatkHuman/higher-vertabrate variant detection toolkit/stor/system/opt/gatk-3.6/
MuTectSomatic Mutations/stor/system/opt/gatk-3.6/
/stor/system/opt/mutect/
plink

GWAS tools

/usr/bin/plink
snpeffGenetic 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.

SoftwareDescriptionPath
mauve

Genome/Transcriptome Assembly Tools

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

SoftwareDescriptionPath
consedcontig assembly tools/usr/local/genome/consed/
phrapcontig assembly tools/usr/local/genome/bin/
phredcontig assembly tools/usr/local/genome/bin/
glimmermicobial gene annotations/usr/bin/glimmer2
/usr/bin/build-icm
/usr/bin/extract
/usr/bin/long-orfs

Web-based application software

The following web application software is available only 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.

SoftwareDescription
JupyterHub Server
Python Notebook Server
R Studio ServerR Studio Web Interface

Special POD software

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
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