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
| 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 BioLinux Packages
| Software | Version | Description |
|---|---|---|
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 |
rasmol | 2.7.5.2-2 | Visualize biological macromolecules |
raxml | 8.2.11+dfsg-1 | Randomized Axelerated Maximum Likelihood of phylogenetic trees |
readseq | 1-12 | Conversion between sequence formats |
rsem | 1.2.31+dfsg-1 | RNA-Seq by Expectation-Maximization |
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 |
sortmerna | 2.1-2 | tool for filtering, mapping and OTU-picking NGS reads |
stacks | 2.0Beta8c+dfsg-1 | pipeline for building loci from short-read sequences |
sumatra | 1.0.31-1 | fast and exact comparison and clustering of sequences |
swarm | 2.2.2+dfsg-1 | robust and fast clustering method for amplicon-based studies |
t-coffee | 2.2.2+dfsg-1 | 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 |
trinityrnaseq | 2.5.1+dfsg-2 | RNA-Seq De novo Assembly |
trnascan-se | 1.3.1-1 | search for tRNA genes in genomic sequences |
velvet | 1.2.10+dfsg1-3build1 | Nucleic acid sequence assembler for very short reads |
velvet-example | 1.2.10+dfsg1-3build1 | Example data for the Velvet sequence assembler |
velvet-long | 1.2.10+dfsg1-3build1 | Nucleic acid sequence assembler for very short reads, long version |
velvetoptimiser | 2.2.6-1 | Automatically optimise Velvet do novo assembly parameters |
vsearch | 2.7.1-1 | tool for processing metagenomic sequences |
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 | GNU R package “Combine multi-dimensional arrays” |
ade4 | GNU R package “Analysis of Ecological Data : Exploratory |
| ape | GNU R package “Analyses of Phylogenetics and Evolution” |
bitops | GNU R package implementing bitwise operations |
catools | GNU R package “Tools: moving window statistics, GIF, |
| cargo | |
cluster | GNU R package for cluster analysis by Rousseeuw et al |
| cowplot | |
| curl | |
data.table | GNU R package “Extension of data.frame” |
dbi | GNU R package “R Database Interface” |
dichromat | Color schemes for dichromats |
digest | GNU R package “Create Cryptographic Hash Digests of R |
evaluate | GNU R package “Parsing and Evaluation Tools that Provide |
| foreach | |
futile.logger | GNU R package “A Logging Utility for R” |
futile.options | GNU R package “Futile options management” |
gdata | GNU R package “Various R Programming Tools for Data |
getopt | GNU R package “C-like getopt behavior.” |
| gganimate | |
| GGally | |
ggplot2 | GNU R package “An Implementation of the Grammar of |
| ggpubr | |
| ggrepel | |
| gifski | |
gplots | GNU R package “Various R Programming Tools for Plotting |
| gridSVG | |
gtable | GNU R package “Arrange grobs in tables.” |
gtools | GNU R package “Various R Programming Tools” |
| igraph | |
| jpeg | |
labeling | GNU R package “Axis Labeling” |
lambda.r | GNU R package “Modeling Data with Functional Programming” |
lattice | GNU R package “Lattice Graphics” |
| leaps | GNU R package “regression subset selection” |
| lme4 | GNU R package for linear mixed effects model fitting |
| lubridate | |
matrix | GNU R package of classes for dense and sparse matrices |
matrixstats | R package “Methods that apply to rows and columns of a matrix” |
| mirbase.db | |
| mixdist | |
| multcomp | |
munsell | GNU R package “Munsell colour system” |
| mvtnorm | |
| network | |
nlme | GNU R package for (non-)linear mixed effects models |
optparse | GNU R package “Command line option parser.” |
permute | GNU R package “Functions for Generating Restricted |
| pheatmap | |
| plotly | |
| plotROC | |
| plotrix | GNU R package “Various plotting functions” |
plyr | GNU R package “Tools for Splitting, Applying and Combining |
proto | GNU R package “Prototype object-based programming” |
| quantmod | |
r.methodss3 | GNU R package “Utility function for defining S3 methods” |
rcolorbrewer | GNU R package providing suitable color palettes |
rcpp | GNU R package “Seamless R and C++ Integration” |
rcurl | GNU R package “General Network (HTTP/FTP/…) Client |
relimp | GNU R package “Relative Contribution of Effects in a |
reshape2 | GNU R package “Flexibly Reshape Data: A Reboot of the |
rggobi | GNU R package for the GGobi data visualization system |
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 |
| RMySQL | |
rserve | GNU R Rserve tcp/ip server and sample clients |
rsqlite | GNU R package “SQLite Interface for R” |
scales | GNU R package “Scale Functions for Visualization” |
scatterplot3d | GNU R package “3D Scatter Plot” |
| sna | |
sp | GNU R package “Classes and Methods for Spatial Data” |
| sqldf | |
stringr | GNU R package “Simple, Consistent Wrappers for Common |
tcltk2 | GNU R package “Tcl/Tk Additions” |
testthat | GNU R package “Testthat code. Tools to make testing fun |
| tidyr | |
vegan | GNU R package “Community Ecology Package” |
| VGAM | |
| vioplot | |
xml | GNU R package “Tools for Parsing and Generating XML Within |
xtable | GNU R coerce data to LaTeX and HTML tables |
Additional R BioConductor Tools
| Software | Description |
|---|---|
| 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 | |
| ballgown | Flexible, 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 |
| BSgenome | Efficient genome searching |
| BSgenome.Hsapiens.UCSC.hg19 | |
| ChIPseeker | annotating ChIP-seq data analysis |
| cummeRbund | analyzing Cufflinks RNA-Seq output |
| deseq | |
| 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 |
| 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 | |
| GOstats | tools 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 | |
| RIPSeeker | identify 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 | |
| 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 | |
xvector | GNU R package “Representation and manpulation of external |
zlibbioc | GNU R package “An R packaged zlib-1.2.5″ |
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 |
| hisat | ||
| fastq_screen | ||
| 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 |
| stringtie | ||
| bwa | Alignment | /usr/bin/bwa |
RNA Sequencing Tools
| Software | Description | Path |
|---|---|---|
| augustus | ||
| busco | ||
| cufflinks | ||
| express | Expression quantification | /usr/bin/express |
| fastqc | ||
| 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 |
| tophat | ||
| 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 |
|---|---|---|
| BWA | ||
| MultiQC | Report Generation | /usr/bin/multiqc |
| eisen cluster | hierachical & k-means clustering | /usr/bin/cluster-eisen |
| imageJ | ||
| 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
Note: These tools are only available on select PODs. At this time of this writing, it included the GSAF and Educational PODs.
| Software | Description | Path |
|---|---|---|
| consed | contig assembly tools | /usr/local/genome/consed/ |
| phrap | contig assembly tools | /usr/local/genome/bin/ |
| phred | contig assembly tools | /usr/local/genome/bin/ |
| glimmer | micobial 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 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.
| Software | Description |
|---|---|
| JupyterHub Server | Python Notebook Server |
| R Studio Server | R Studio Web Interface |
Special POD software
The following software is available only on specific PODs or nodes of a pod.
| Software | Description | Location | Path |
|---|---|---|---|
| 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 | ||
| irodsfs | Not yet fully supported | gsafcbig01 | /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 |