...
All POD compute servers have (nearly) identical Ubuntu 1820.04 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 And some PODs also have additional software installed which that is unique to that POD.Let us know if there is additional software you would like to have installed.
Installing software
Users can perform local (per-user) installations that do not require administrative (root/sudo) access. For software that does require sudo, or if you would like a package installed globally for use by others, please email us at rctf-support@utexas.edu.
Programs in /stor/system/opt
Some tool "suites" that have many sub-program binaries, are not made available on the standard PATH. The /stor/system/opt directory on your system contains installation directories for these tools, which can be added to your PATH as needed. Examples include multiple versions of the sratoolkit and the picard-tools suites. E.g.:
| Code Block | ||
|---|---|---|
| ||
export PATH="/stor/system/opt/sratoolkit.2.8.2-ubuntu64/bin:$PATH" |
Programs in /mnt/bioi/tools
All compute servers have a shared, read-only /mnt/bioi directory mounted that contains many useful bioinformatics resources such as annotations and other references in /mnt/bioi/ref_genome and external data in /mnt/bio/data).T
Specifically, the /mnt/bioi/tools directory contains several tool suites and their associated data (e.g. cellranger, GSEA), and each tool suite directory has multiple tool version sub-directories. Like the suites in /stor/system/opt, the associated binaries are not on your PATH by default, but can be added as needed, e.g.:
| Code Block | ||
|---|---|---|
| ||
export PATH="/mnt/bioi/tools/cellranger/8.0.0/bin":$PATH
export PATH="/mnt/bioi/tools/UCSC_utils/2023_08:$PATH" |
Multiple software versions
Unlike TACC, we do not implement a module system. Rather, we install different versions of a program side-by-side, with names differing by their versions (for example:
- Rscript (the default version, same as Rscript-4-3.1), Rscript-4.3.1, Rscript-4.0.3, Rscript-3.6.3
- samtools (the default, version 1.10), samtools-1.9, samtools-1.11
In particular, multiple versions of R and Python are installed side-by-side. For more information, see:
Often you can see if there are multiple versions of a program installed just by typing its name and hitting the Tab key twice. For example, typing bedtools then Tab Tab shows this:
| Code Block |
|---|
bedtools bedtools-2.25.0 bedtools-2.26.0 bedtools-2.27.1 bedtools-2.28.0 |
Web-based application R Studio and Python JupyterHub 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. See also About R and R Studio Server and About Python and JupyterHub server help pages.
| Software | Description | Access |
|---|---|---|
| JupyterHub Server | Python Notebook Server | Available on all compute servers https://<server_name>.ccbb.utexas.edu |
| R Studio Server | R Studio Web Interface |
...
| R Studio Server | R Studio Web Interface |
After the August 2023 maintenance, all POD compute servers now use R 4.3.1 as the R version in their RStudio Server web application. If your POD has multiple compute servers and you would like one to run a different R version, please contact us at rctf-support@utexas.edu.
Standard OS Software
(to find in repo: frep -r pattern .| grep -v /spec/)
| 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. |
| scons | Software build tool |
| swig | Software development tool |
| sqlite3 | SQL Lite databases |
| git | Version control utilities |
Standard BioLinux Packages
...
(find using: dpkg -l bioperl)
...
R modules in repo common.yaml
| Software | Version | Description | in cqb-biolinux? |
|---|---|---|---|
2.0.2-3 | de novo, parallel, sequence assembler for short reads | y | |
bamtools | 2.4.1+dfsg-2 | toolkit for manipulating BAM (genome alignment) files | y |
bedtools | 2.26.0+dfsg-5 | suite of utilities for comparing genomic features y | |
| bioperl | 1.7.2-2 | Perl tools for computational molecular biology y | |
bioperl-run | 1.7.1-3 | BioPerl wrappers: scripts | y |
| blast2 | 1:2.6.0-1 | Basic Local Alignment Search Tool y | |
| bowtie | 1.2.2+dfsg-2 | Ultrafast memory-efficient short read aligner y | |
| bowtie2 | 2.3.4.1-1 | Ultrafast memory-efficient short read aligner | n |
| bwa | 0.7.17-1ubuntu0.1 | Burrows-Wheeler Aligner | n |
| cd-hit | 4.6.8-1 | a suite of programs designed to quickly group sequences y | |
clustalw | 2.1+lgpl-5 | No description y | |
clustalx | 2.1+lgpl-6 | No description | y |
cufflinks | 2.2.1+dfsg.1-2 | Transcript assembly, differential expression and regulation for RNA-Seq n | |
| diamond | 2.0.14 | sequence aligner for protein and translated DNA searches | |
| DiffBind | 3.0.15 | Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data | |
ea-utils | 1.1.2+dfsg-4build1 | command-line tools for processing biological sequencing data | y |
emboss | 6.6.0+dfsg-6build1 | european molecular biology open software suite n | |
emboss-lib | 6.6.0+dfsg-6build1 | EMBOSS Libraries | y |
fastdnaml | 1.2.2-12 | Tool for construction of phylogenetic trees of DNA sequences | y |
fastqc | 0.11.5+dfsg-6 | A quality control application for high throughput sequence data | n |
fastx-toolkit | 0.0.14-5 | FASTQ/A short nucleotide reads pre-processing tools | y |
hmmer | 3.1b2+dfsg-5ubuntu1 | profile hidden Markov models for protein sequence analysis | n |
jaligner | 1.0+dfsg-4 | Smith-Waterman algorithm with Gotoh’s improvement y | |
jellyfish | 2.2.8-3build1 | count k-mers in DNA sequences y | |
khmer | 2.1.2+dfsg-3 | kk0.7.17-1ubuntu0.1-mer counting, filtering and graph traversal | y |
libbiojava-java | 1:1.7.1-7 | Java API to biological data and applications (default version) y | |
libbiojava-java-demos | 1:1.7.1-7 | Example programs for BioJava y | |
macs | 2.1.1.20160309-2 | Model-based Analysis of ChIP-Seq on short reads sequencers | y |
mafft | 7.310-1 | Multiple alignment program for amino acid or nucleotide sequences | y |
maq | 0.7.1-7 | maps short fixed-length polymorphic DNA sequence reads to reference sequences | y |
| med-bioy | 3.0.1ubuntu1 | Debian Med bioinformatics packages | |
| med-cloudy | 3.0.1ubuntu1 | Debian Med bioinformatics applications usable in cloud computing | |
microbiomeutil | 20101212+dfsg1-1build1 | Microbiome Analysis Utilities y | |
| minfi | 1.24.0 | Analyze Illumina Infinium DNA methylation arrays | |
mothur | 1.39.5-2build1 | sequence analysis suite for research on microbiota y | |
mothur-mpi | 1.39.5-2build1 | mpi-enabled binary for mothur | y |
mrbayes-mpi | 3.2.6+dfsg-2 | Bayesian Inference of Phylogeny – mpi version | y |
mummer | 3.23+dfsg-3 | Efficient sequence alignment of full genomes | y |
muscle | 1:3.8.31+dfsg-3 | Multiple alignment program of protein sequences | y |
ncbi-blast+ | 2.6.0-1 | next generation suite of BLAST sequence search tools | n |
ncbi-blast+-legacy | 2.6.0-1 | NCBI Blast legacy call script n | |
ncbi-seg | 0.0.20000620-4 | tool to mask segments of low compositional complexity in amino acid sequences y | |
ncbi-tools-bin | 6.1.20170106-2 | NCBI libraries for biology applications (text-based utilities) | y |
ncbi-tools-x11 | 6.1.20170106-2 | NCBI libraries for biology applications (X-based utilities) y | |
paml | 4.9g+dfsg-3 | Phylogenetic Analysis by Maximum Likelihood (PAML) | y |
parafly | 0.0.2013.01.21-3build1 | parallel command processing using OpenMP y | |
phylip | 1:3.696+dfsg-5 | No description y | |
phyml | 3:3.3.20170530+dfsg-2 | Phylogenetic estimation using Maximum Likelihood | y |
picard-tools | 2.8.1+dfsg-3 | Command line tools to manipulate SAM and BAM files y | |
primer3 | 2.4.0-1ubuntu2 | Tool to design flanking oligo nucleotides for DNA amplification | y |
pymol | 1.8.4.0+dfsg-1build1 | Molecular Graphics System | y |
qiime | 3:3.3.20170530+dfsg-2 (1.8.0+dfsg-4ubuntu1)? | Quantitative Insights Into Microbial Ecology | y |
rasmol | 2.7.5.2-2 | Visualize biological macromolecules | y |
raxml | 8.2.11+dfsg-1 | Randomized Axelerated Maximum Likelihood of phylogenetic trees y | |
readseq | 1-12 | Conversion between sequence formats y | |
rsem | 1.2.31+dfsg-1 | RNA-Seq by Expectation-Maximization y | |
| Rsubread | 2.4.3 | Mapping, quantification and variant analysis of sequencing data | |
samtools | 1.7-1 | processing sequence alignments in SAM and BAM formats | n |
sift | 4.0.3b-6 | predicts if a substitution in a protein has a phenotypic effect | y |
sortmerna | 2.1-2 | tool for filtering, mapping and OTU-picking NGS reads y | |
stacks | 2.0Beta8c+dfsg-1 | pipeline for building loci from short-read sequences y | |
sumatra | 1.0.31-1 | fast and exact comparison and clustering of sequences | y |
swarm | 2.2.2+dfsg-1 | robust and fast clustering method for amplicon-based studies | y |
t-coffee | 2.2.2+dfsg-1-1 (11.00.8cbe486-6) | Multiple Sequence Alignment n | |
tophat | 2.1.1+dfsg1-1 | fast splice junction mapper for RNA-Seq reads n | |
transdecoder | 5.0.1-1 | find coding regions within transcripts | y |
trinityrnaseq | 2.5.1+dfsg-2 | RNA-Seq De novo Assembly y | |
trnascan-se | 1.3.1-1 | search for tRNA genes in genomic sequences | y |
velvet | 1.2.10+dfsg1-3build1 | Nucleic acid sequence assembler for very short reads y | |
velvet-example | 1.2.10+dfsg1-3build1 | Example data for the Velvet sequence assembler | |
velvet-examplelong | 1.2.10+dfsg1-3build1 | Example data for the Velvet sequence assembler | y |
velvet-long | 1.2.10+dfsg1-3build1 | Nucleic acid sequence assembler for very short reads, long version | y |
velvetoptimiser | 2.2.6-1 | Automatically optimise Velvet do novo assembly parameters | y |
vsearch | 2.7.1-1 | tool for processing metagenomic sequences | y | zsh | y |
Standard Third-Party Software (versions?)
...
Additional Development Tools (move to regular)
...
Additional Python Tools (cqb-devel_tools/manifests/python.pp) find version with pip
| Software | Description | in devel_tools | all-dev | y |
|---|---|---|---|
| blaze | An interface to query data on different storage systems | y | |
| cutadapt | Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads | y | |
| dendropy | phylogenetic computing | y | freetype-dev (libfreetype6-dev) | y | leukgen-disambiguate | y |
| MACS2 | Model Based Analysis for ChIP-Seq data | y | maplot | y |
| matplotlib | python 2D plotting library | y | |
| networkx | Creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | y | |
| nimfa | Nonnegative matrix factorization | y | |
| numpy | scientific computing with Python | y | |
| pandas | Python Data Analysis Library | y | patsy | y |
| pip | Python installation program (to install python modules) | y | plotly | y | pysam | y | pyvttbl | y | reportlab (->biopython?) | y |
| rpy2 | Python interface to R | y | |
| seaborn | y | scipy +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 | |
| zsh | 5.4.2-3ubuntu3.1 | shell with lots of features |
Standard Third-Party Software (versions?)
| Software | Description | Version |
|---|---|---|
| R, Rscript | R command-line shell and script execution programs. | 3.4.4, 3.5.3, 3.6.1 |
| Matlab | MathWorks Matlab Software. See How do I use MATLAB on the POD? | |
| docker | OS-level virtualization to deliver software in packages called containers | |
| singularity | Containerization software for scientific data |
Additional Python Tools
(in repo under cqb-devel_tools/manifests/python.pp) find version with pip (pip3 freeze | grep xopen)
| Software | Python2 Version | Python3 Version | Description | ||
|---|---|---|---|---|---|
| all-dev | |||||
| blaze | 0.10.1 | 0.10.1 | An interface to query data on different storage systems | ||
| cutadapt | 1.18 | 1.18 | Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads | ||
| dendropy | phylogenetic computing | ||||
| freetype-dev (libfreetype6-dev) | This package contains all of the supplementary files you need to develop your own programs using the FreeType 2 library. | ||||
| leukgen-disambiguate | 1.0.1 | 1.0.1 | Disambiguate reads mapping to multiple genomes. This is a frozen release with some bug fixes of the original AstraZeneca-NGS/disambiguate v1.0. | ||
| MACS2 | 2.1.2 | Model Based Analysis for ChIP-Seq data | |||
| maplot | 1.0.2 | 1.0.2 | Python package for creating interactive MA-plots | ||
| matplotlib | 2.1.1 | 3.2.1 | python 2D plotting library | ||
| networkx | 2.2 | 2.0 | Creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | ||
| nimfa | 1.3.4 | 1.3.4 | Nonnegative matrix factorization | ||
| numpy | 1.13.3 | 1.13.3 | scientific computing with Python | ||
| pandas | 0.22.0 | 0.22.0 | Python Data Analysis Library | ||
| patsy | 0.4.1+dev | 0.2.1 | Patsy is a Python library for describing statistical models (especially linear models, or models that have a linear component) and building design matrices. Patsy brings the convenience of R “formulas” to Python. | ||
| pip | Python installation program (to install python modules) | ||||
| plotly | 4.0.0 | 4.0.0 | An open-source, interactive data visualization library for Python | ||
| pysam | 0.8.4 | 0.8.4 | a python module for reading, manipulating and writing genomic data sets | ||
| pyvttbl | 0.5.2.2 | 0.5.2.2 | Multidimensional pivot tables, data processing, statistical computation | ||
| reportlab (->biopython?) | 3.4.0 (->1.70) | 3.5.12 (->1.73) | The ReportLab Toolkit. An Open Source Python library for generating PDFs and graphics. (→ Freely available tools for computational molecular biology) | ||
| rpy2 | 2.8.6 | 2.9.2 | Python interface to R | ||
| seaborn | 0.8.1 | 0.8.1 | statistical data visualization | ||
| scipy | 0.19.1 | 0.19.1 | Collection of Python software for mathematics, science, and engineering. | y | |
| sklearn | Machine Learning in Python | y||||
| skimage | Image processing in Python | y | statsmodels|||
| statsmodels | 0.8.0 | 0.8.0 | Estimation of statistical modelsy | ||
| pytorch/torch | 1.7.0 | 1.7.0 | Optimized tensor library for deep learning | ||
torchvision | 0.8.1 | 0.8.1 | popular datasets, model architectures, and common image transformations for computer vision |
Additional R Tools
(in repo cqbhiera/common.yaml)
| Software | Description | in common.yaml|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| abind | GNU R package “Combine multi-dimensional arrays” | y|||||||||||
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 | |||||||||||
| blogdowny | Create Blogs and Websites with R Markdown | |||||||||||
| bookdowny | Authoring Books and Technical Documents with R Markdown | |||||||||||
catools | GNU R package “Tools: moving window statistics, GIF, y | |||||||||||
| cary | Companion to Applied Regression | |||||||||||
| cargo | y | |||||||||||
cluster | GNU R package for cluster analysis by Rousseeuw et al | |||||||||||
| colourpickery | A Colour Picker Tool for Shiny and for Selecting Colours in Plots | |||||||||||
| cowploty | Streamlined Plot Theme and Plot Annotations for 'ggplot2' | |||||||||||
| curly | A Modern and Flexible Web Client for R | |||||||||||
data.table | GNU R package “Extension of data.frame” | |||||||||||
dbi | GNU R package “R Database Interface” | |||||||||||
| dbplyr | y | dendextend | R Database Interface | |||||||||
| dendextend | Extending 'dendrogram' Functionality in R | |||||||||||
dichromat | Color schemes for dichromats | |||||||||||
digest | GNU R package “Create Cryptographic Hash Digests of R | |||||||||||
| emmeansy | Estimated Marginal Means, aka Least-Squares Means | |||||||||||
evaluate | GNU R package “Parsing and Evaluation Tools that Provide | |||||||||||
| fivethirtyeighty | Data and Code Behind the Stories and Interactives at 'FiveThirtyEight' | |||||||||||
| forcatsy | Data and Code Behind the Stories and Interactives at 'FiveThirtyEight' | |||||||||||
| foreachy | Provides Foreach Looping Construct | |||||||||||
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.” | |||||||||||
| gganimatey | A Grammar of Animated Graphics | |||||||||||
| GGallyy | Extension to 'ggplot2' | |||||||||||
| ggExtray | Add Marginal Histograms to 'ggplot2', and More 'ggplot2' Enhancements | |||||||||||
ggplot2 | GNU R package “An Implementation of the Grammar of | |||||||||||
| ggpubr | y | ggrepel | y | ggsci | y | ggsignif | y | gifski | y | glmnet | y | 'ggplot2' Based Publication Ready Plots |
| ggrepel | Automatically Position Non-Overlapping Text Labels with 'ggplot2' | |||||||||||
| ggsci | Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2' | |||||||||||
| ggsignif | Significance Brackets for 'ggplot2' | |||||||||||
| gifski | Highest Quality GIF Encoder | |||||||||||
| glmnet | Lasso and Elastic-Net Regularized Generalized Linear Models | |||||||||||
gplots | GNU R package “Various R Programming Tools for Plotting | |||||||||||
| gridSVGy | Export 'grid' Graphics as SVG | |||||||||||
| gt | Build display tables from tabular data with an easy-to-use set of functions | |||||||||||
gtable | GNU R package “Arrange grobs in tables.” | |||||||||||
gtools | GNU R package “Various R Programming Tools” | |||||||||||
| haveny | Import and Export 'SPSS', 'Stata' and 'SAS' Files | |||||||||||
| igraphy | Network Analysis and Visualization | |||||||||||
| interactionsy | Comprehensive, User-Friendly Toolkit for Probing Interactions | |||||||||||
| jpegy | Read and write JPEG images | |||||||||||
labeling | GNU R package “Axis Labeling” | |||||||||||
lambda.r | GNU R package “Modeling Data with Functional Programming” | |||||||||||
lattice | GNU R package “Lattice Graphics” | |||||||||||
| latticeExtray | Extra Graphical Utilities Based on Lattice | |||||||||||
| leaps | GNU R package “regression subset selection” | y | ||||||||||
| libssl-dev | prereq?y | |||||||||||
| libcairo2-dev | perreq?y | |||||||||||
| libxt-dev | prereq? | y | ||||||||||
| libgmp10 | prereq?y | |||||||||||
| libgmp-dev | prereq? | y | ||||||||||
| libmpfr6 | prereq? | y | ||||||||||
| libmpfr-dev | prereq? | y | ||||||||||
| lme4 | GNU R package for linear mixed effects model fitting | y | locfit | y | lubridate | |||||||
| ylocfit | Local Regression, Likelihood and Density Estimation | |||||||||||
| lubridate | Make Dealing with Dates a Little Easier | |||||||||||
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 | miRBase: the microRNA database | |||||||||||
| mixdisty | Finite Mixture Distribution Models | |||||||||||
| modelry | Modelling Functions that Work with the Pipe | |||||||||||
| multcompy | Simultaneous Inference in General Parametric Models | |||||||||||
munsell | GNU R package “Munsell colour system” | |||||||||||
| mvtnormy | Multivariate Normal and t Distributions | |||||||||||
| networky | Classes for Relational Data | |||||||||||
nlme | GNU R package for (non-)linear mixed effects models | |||||||||||
| nloptry | R Interface to NLopt | |||||||||||
| ontologyIndexy | Functions for Reading Ontologies into R | |||||||||||
optparse | GNU R package “Command line option parser.” | |||||||||||
permute | GNU R package “Functions for Generating Restricted | |||||||||||
| pheatmapy | Pretty Heatmaps | |||||||||||
| pbkrtest | y | plotly | y | plotROC | y Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison | |||||||
| plotly | Create Interactive Web Graphics via 'plotly.js' | |||||||||||
| plotROC | Generate Useful ROC Curve Charts for Print and Interactive Use | |||||||||||
| plotrix | GNU R package “Various plotting functions” y | |||||||||||
plyr | GNU R package “Tools for Splitting, Applying and Combining | |||||||||||
| polynomy | A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations | |||||||||||
proto | GNU R package “Prototype object-based programming” | y | ||||||||||
| quantmody | Quantitative Financial Modelling Framework | |||||||||||
| quantregy | Quantile Regression | |||||||||||
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 | y | ||||||||||
reshape2 | GNU R package “Flexibly Reshape Data: A Reboot of the y | |||||||||||
| reticulatey | Interface to 'Python' | |||||||||||
rggobi | GNU R package for the GGobi data visualization system | y | ||||||||||
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 y | |||||||||||
| RMySQLy | Database Interface and 'MySQL' Driver for R | |||||||||||
| ROCRy | Visualizing the Performance of Scoring Classifiers | |||||||||||
rserve | GNU R Rserve tcp/ip server and sample clients | y | ||||||||||
| rstatix | yrstatix | Pipe-Friendly Framework for Basic Statistical Tests | ||||||||||
rsqlite | GNU R package “SQLite Interface for R” | |||||||||||
| rvesty | Easily Harvest (Scrape) Web Pages | |||||||||||
scales | GNU R package “Scale Functions for Visualization” | |||||||||||
scatterplot3d | GNU R package “3D Scatter Plot” y | |||||||||||
| servry | A Simple HTTP Server to Serve Static Files or Dynamic Documents | |||||||||||
| Seurat | y | shape | y | shiny | y | shinyjs | y | sna | yTools for Single Cell Genomics | |||
| shape | Functions for Plotting Graphical Shapes, Colors | |||||||||||
| shiny | Web Application Framework for R | |||||||||||
| shinyjs | Easily Improve the User Experience of Your Shiny Apps in Seconds | |||||||||||
| showtext | Making it easy to use various types of fonts in R graphs | |||||||||||
| showtextdb | Providing font files that can be used by the 'showtext' package | |||||||||||
| Signac | A framework for the analysis of single-cell chromatin data | |||||||||||
| sna | Tools for Social Network Analysis | |||||||||||
sp | GNU R package “Classes and Methods for Spatial Data” | |||||||||||
| sqldfy | Manipulate R Data Frames Using SQL | |||||||||||
| statnet.commony | Common R Scripts and Utilities Used by the Statnet Project Software | |||||||||||
stringr | GNU R package “Simple, Consistent Wrappers for Common | |||||||||||
| sysfonts | Loading system fonts and Google Fonts into R | |||||||||||
tcltk2 | GNU R package “Tcl/Tk Additions” | y | ||||||||||
testthat | GNU R package “Testthat code. Tools to make testing fun | |||||||||||
| tibbley | Simple Data Frames | |||||||||||
| tidyr | Tidy Messy Data | y | ||||||||||
| tidyversey | Easily Install and Load the 'Tidyverse' | |||||||||||
| transformry | Polygon and Path Transformations | |||||||||||
vegan | GNU R package “Community Ecology Package” | |||||||||||
| VennDiagramy | Generate High-Resolution Venn and Euler Plots | |||||||||||
| VGAMy | Vector Generalized Linear and Additive Models | |||||||||||
| vioplot | yViolin Plot | |||||||||||
| xfuny | Miscellaneous Functions by 'Yihui Xie' | |||||||||||
xml | GNU R package “Tools for Parsing and Generating XML Within y | |||||||||||
xtable | GNU R coerce data to LaTeX and HTML tables |
Additional R BioConductor Tools
(in repo cqbhiera/common.yaml)
| Software | Description | |
|---|---|---|
| affyy | Methods for Affymetrix Oligonucleotide Arrays | |
| affyio | GNU R package “Tools for parsing Affymetrix data files” | |
| annotate | GNU R package “Annotation for microarrays” | |
annotationdbi | GNU R package “Annotation Database Interface” | |
| arrayQualityMetricsy | Quality metrics report for microarray data sets | |
| ballgown | Flexible, isoform-level differential expression analysisy | |
| 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 | y |
| BSgenome.Hsapiens.UCSC.hg19y | Full genome sequences for Homo sapiens (UCSC version hg19) | |
| ChIPseeker | annotating ChIP-seq data analysis | y |
| cummeRbund | analyzing Cufflinks RNA-Seq outputy | |
| 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 | y |
| devtools | Collection of package development tools | y |
| DEXSeq | finding differential exon usage using RNA-seq exon counts between samples | y | 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 | ggplot2movies | GISPA | y |
| GOstats | tools for interacting with GO and microarray data | y | GO.db | y | hilbertvis | GNU R package to visualise long vector data | httpuv | y | iranges | GNU R package “Infrastructure for manipulating intervals | JunctionSeq | y | limma | GNU R package “Linear Models for Microarray Data” | mirbase.db | y | multtest | GNU R package “Resampling-based multiple hypothesis | org.Hs.eg.db | y | org.Sc.sgd.db | y | org.Mm.eg.db | y | org.Rn.eg.db | y | preprocesscore | GNU R package “A collection of pre-processing functions” | processx | y | pkgload | y | qvalue | Bioconductor package “Q-value estimation for false discovery rate control” |
| rhdf5 | provides an interface between HDF5 and R | y | readr | y | ReportingTools | y |
| RIPSeeker | identify protein-associated transcripts from RIP-seq experiments | y | roxygen2 | y | rsamtools | GNU R package “Binary alignment (BAM), variant call (BCF), | s4vectors | GNU R package “S4 implementation of vectors and lists” | SISPA | y |
| sleuth | analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto | y |
| ShortRead | sampling, iteration, and input of FASTQ files | y | topGO | y | TxDb.Scerevisiae.UCSC.sacCer3.sgdGene | y | TxDb.Hsapiens.UCSC.hg38.knownGene | y | tximport | y | WGCNA | y | xvector | GNU R package “Representation and manpulation of external | yardstick | y | zlibbioc | GNU R package “An R packaged zlib-1.2.5″ |
Additional Perl CPAN modules (cqbprofile/manifest/perl.pp and cqb-maker)
...
| the negative binomial distribution | |
| devtools | Collection of package development tools |
| DEXSeq | finding differential exon usage using RNA-seq exon counts between samples |
| EnhancedVolcano | Publication-ready volcano plots with enhanced colouring and labeling |
| genefilter | 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 |
| ggplot2movies | Movies Data |
| GISPA | GISPA: Method for Gene Integrated Set Profile Analysis |
| GOstats | tools for interacting with GO and microarray data |
| GO.db | |
hilbertvis | GNU R package to visualise long vector data |
| httpuv | HTTP and WebSocket Server Library |
iranges | GNU R package “Infrastructure for manipulating intervals |
| JunctionSeq | JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data |
limma | GNU R package “Linear Models for Microarray Data” |
| mirbase.db | miRBase: the microRNA database |
multtest | GNU R package “Resampling-based multiple hypothesis |
| org.Hs.eg.db | Genome wide annotation for Human |
| org.Sc.sgd.db | Genome wide annotation for Yeast |
| org.Mm.eg.db | Genome wide annotation for Mouse |
| org.Rn.eg.db | Genome wide annotation for Rat |
preprocesscore | GNU R package “A collection of pre-processing functions” |
| processx | Execute and Control System Processes |
| pkgload | |
| qvalue | Bioconductor package “Q-value estimation for false discovery rate control” |
| rhdf5 | provides an interface between HDF5 and R |
| readr | Read Rectangular Text Data |
| ReportingTools | Tools for making reports in various formats |
| RIPSeeker | identify protein-associated transcripts from RIP-seq experiments |
| roxygen2 | In-Line Documentation for R |
| rsamtools | GNU R package “Binary alignment (BAM), variant call (BCF), |
s4vectors | GNU R package “S4 implementation of vectors and lists” |
| SISPA | SISPA: Method for Sample Integrated Set Profile Analysis |
| sleuth | analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto |
| ShortRead | sampling, iteration, and input of FASTQ files |
| topGO | Enrichment Analysis for Gene Ontology |
| TxDb.Scerevisiae.UCSC.sacCer3.sgdGene | Annotation package for TxDb object(s) |
| TxDb.Hsapiens.UCSC.hg38.knownGene | Annotation package for TxDb object(s) |
| tximport | Import and summarize transcript-level estimates for transcript- and gene-level analysis |
| WGCNA | Weighted Correlation Network Analysis |
xvector | GNU R package “Representation and manpulation of external |
| yardstick | Tidy Characterizations of Model Performance |
zlibbioc | GNU R package “An R packaged zlib-1.2.5″ |
Additional Perl CPAN modules
(in repo cqbprofile/manifest/perl.pp and cqb-maker)
| Software | Description |
|---|---|
| Bit::Vector | |
| CGI | |
| DBI | |
| DBD::SQLite | |
| File::Which | |
| forks | |
| forks::shared | |
| Graph | |
| IO::All | |
| IO:Prompt | |
| LWP | |
| Math::Cephes | |
| Module::Build | |
| Net::HTTP | |
| Perl::Unsafe::Signals | |
| Statistics::Descriptive | |
| Switch | |
| Test::Class | |
| Test::More | |
| Test::Exception | |
| Test::Harness | |
| XML::Simple |
Next Generation Sequencing (NGS) Tools
(in repo cqbprofile/manifest/next_gen_sequencing_client.pp)
| Software | Description | Path |
|---|---|---|
| bamtools | SAM/BAM file manipulation | /stor/system/opt/gitdir/bamtools/bin/bamtools |
| bcl2fastq | BCL file manipulation | /usr/bin/bcl2fastq |
| deeptools | ||
| enabrowsertools | ||
| hisat | ||
| fastq_screen | ||
| guppy | ||
| 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 |
| samtools | ||
| scalangs | ||
| sra toolkit | SRA file manipulation | /stor/system/opt/sratoolkit.2.7.0-ubuntu64 |
| stringtie | ||
| bwa | Alignment | /usr/bin/bwa |
RNA Sequencing Tools
(in repo cqbprofile/manifest/rna_sequencing_client.pp)
| Software | Description | Path | in next_gen_sequencing_client.pp | bamtools | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| augustus | program to find genes and their structures in one or more genomes | |||||||||
| busco | ||||||||||
| cellranger | ||||||||||
| cufflinks | ||||||||||
| express | Expression quantification | /usr/bin/express | ||||||||
| fastqc | ||||||||||
| featurecounts | Counting | /usr/bin/featureCounts | ||||||||
| htseq | Counting | /stor/system/opt/gitdir/bamtools/bin/bamtools | y | bcl2fastq | BCL file manipulationHTSeq-0.6.1p1 | |||||
| kallisto | Expression quantification | /usr/bin/bcl2fastqkallisto | y | deeptools | y | enabrowsertools | y | hisat | y | fastq_screen |
| guppy | y | samtools | SAM/BAM file manipulationSTAR | Alignment | /usr/bin/samtoolsSTAR /usr/bin/samtools_0.1.18STARlong | |||||
| tophat | ||||||||||
| MultiQC | Report Generation | /usr/bin/samtools-1.3 | picard | SAM/BAM file manipulation | multiqc | |||||
| RNA-SeQC | QC of RNA-seq alignments. To run this Java program: java -jar /stor/system/opt/picard-tools-1.141rnaseqc/RNA-SeQC_v1.1.8.jar <other options> | /stor/system/opt/picard-tools-2.5.0 | y | |||||||
bedtools | BED/GFF file manipulation | /usr/bin/bedtools-2.17.0 /usr/bin/bedtools-2.25.0 | y | |||||||
| samtools | y | scalangs | y | sra toolkit | SRA file manipulationrnaseqc | |||||
| salmon | ||||||||||
| 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/sratoolkit.hisat2-2.7.0-ubuntu64 | y | stringtie | y | bwa | Alignment | /usr/bin/bwa |
...
| 0.5/ | ||
| gossamer | bioinformatics suite including goss, gossple, xenome, and electus | /usr/local/bin/goss /usr/local/bin/gossple /usr/local/bin/xenome /usr/local/bin/electus |
Specialized NGS Tools
(in repo specialized_sequencing_client.pp)
| Software | Description | Path | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BWA | in rna_sequencing_client.pp | augustus | y | busco | y | cellranger | y | cufflinks | y | express | Expression quantification | |||||
| bwa_mem2 | ||||||||||||||||
| MultiQC | Report Generation | /usr/bin/express | y | fastqc | y | featurecounts | Countingmultiqc | |||||||||
| eisen cluster | hierachical & k-means clustering | /usr/bin/featureCountscluster-eisen | ||||||||||||||
| yimageJ | ||||||||||||||||
| htseqmeme suite | Countingmotif analysis | /stor/system/opt/HTSeq-0.6.1p1 | y | |||||||||||||
| kallisto | Expression quantification | /usr/bin/kallisto | y | |||||||||||||
| STAR | Alignmentmeme_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/STARart_454 /usr/bin/STARlong | y | tophat | y | MultiQC | Report Generation | art_illumina /usr/bin/multiqc | y | RNA-SeQC | QC of RNA-seq alignments. To run this Java program:/stor/system/opt/rnaseqc | y | salmon | y | hisat | Spliced alignment for mapping RNA-seq readsart_SOLiD |
Variant Analysis Tools (variant_analysis_client.pp)
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/hisat-0.1.6-beta | hisat2 | Align NGS reads (both DNA and RNA) against a reference genomeannovar/ |
| gatk | Human/higher-vertabrate variant detection toolkit | /stor/system/opt/hisat2gatk-23.0.56/ |
Specialized NGS Tools (specialized_sequencing_client.pp)
| Software | Description | Path | in specialized_sequencing_client.pp | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| BWA | y | bwa_mem2 | y | MultiQC | Report Generation | /usr/bin/multiqc | eisen cluster | hierachical & k-means clusteringMuTect | Somatic Mutations | /stor/system/opt/gatk-3.6/ /stor/system/opt/mutect/ |
| plink | GWAS tools | /usr/bin/cluster-eisenplink | y | imageJ | y | |||||
| meme suite | motif analysis | snpeff | Genetic variant annotation and effect prediction | /stor/system/opt/meme_4.11.2 | ||||||
| meme_chip | motif analysis suite for ChIP-seq | /stor/system/opt/software/meme-chip/4.11.2/ | y | |||||||
| art | next generation sequencing read simulator | /usr/bin/art_454 /usr/bin/art_illumina /usr/bin/art_SOLiD | y |
Variant Analysis Tools (variant_analysis_client.pp)
...
| snpEff |
Evolutionary Analysis Tools (evolution_sequencing_client.pp)
Note: These tools are only available on select PODs. At this time of this writing, it included the GSAF POD.
| Software | Description | Path | in evolution_sequencing_client.pp? |
|---|---|---|---|
| mauve | y |
Genome/Transcriptome Assembly Tools genome_client.pp
Note: These tools are only available on select PODs. At this time of this writing, it included the GSAF and Iyer Educational PODs.
| Software | Description | Path | in variant_analysis_client.pp |
|---|---|---|---|
| annovar | Annotation of variants | /stor/system/opt/annovar/ | y |
| gatk | Human/higher-vertabrate variant detection toolkit | /stor/system/opt/gatk-3.6/ | y |
| MuTect | Somatic Mutations | /stor/system/opt/gatk-3.6/ /stor/system/opt/mutect/ | y |
| plink | GWAS toolsconsed | 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/plink | y |
| snpeff | Genetic variant annotation and effect prediction | /stor/system/opt/snpEff | y |
Evolutionary Analysis Tools (evolution_sequencing_client.pp)
Note: These tools are only available on select PODs. At this time of this writing, it included the GSAF POD.
...
Genome/Transcriptome Assembly Tools genome_client.pp
...
| glimmer2 /usr/bin/build-icm /usr/bin/extract /usr/bin/long-orfs | ||
| ISEScan | identification of insertion sequence elements in genomes | /usr/lib/libssw.so |
| FragGeneScan | requirement of ISEScan | /usr/bin/FragGeneScan1.30 |
Molecular Structures Client
| Software | Description | Path | in genome_client.pp |
|---|---|---|---|
| consed | contig assembly tools | /usr/local/genome/consed/ | y |
| phrap | contig assembly tools | /usr/local/genome/bin/ | y |
| phred | contig assembly tools | /usr/local/genome/bin/ | y |
| glimmer | micobial gene annotations | /usr/bin/glimmer2 /usr/bin/build-icm /usr/bin/extract /usr/bin/long-orfs | y |
| gromacs | package to perform molecular dynamics | ||
| mgltools | software for visualization and analysis of molecular structures | ||
| nwchem | computes properties of molecular and periodic systems |
Other software Packages
| Software | Descripition | Path | puppet file |
|---|---|---|---|
| tensorflow | platform for machine learning | python | compute_server.pp |
| keras | high-level API of TensorFlow | python | compute_server.pp |
POD-specific software (look for these)
...
| 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 |
...