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 |
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 |
| 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 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.
| 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 |