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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/system/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
languagebash
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
languagebash
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.

SoftwareDescriptionAccess
JupyterHub Server
Python Notebook Server

Available on all compute servers

https://<server_name>.ccbb.utexas.edu
(e.g. https://gsafcomp01.ccbb.utexas.edu)

R Studio ServerR Studio Web Interface

The current version of R used for R Studio Server is 3.6.1 on most compute servers. However R 4.0.3 is the R version on these compute servers:

.utexas.edu
(e.g. https://

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)

R Studio ServerR 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/)

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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

bwa0.7.17-1ubuntu0.1

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

diamond2.0.14sequence aligner for protein and translated DNA searches
DiffBind3.0.15Compute 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

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

k0.7.17-1ubuntu0.1-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

med-bio3.0.1ubuntu1Debian Med bioinformatics packages
med-cloud3.0.1ubuntu1

Debian Med bioinformatics applications usable in cloud computing

microbiomeutil

20101212+dfsg1-1build1

Microbiome Analysis Utilities

minfi1.24.0

Analyze Illumina Infinium DNA methylation arrays

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 (1.8.0+dfsg-4ubuntu1)?

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

Rsubread2.4.3

Mapping, quantification and variant analysis of sequencing data

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 (11.00.8cbe486-6)

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

zsh5.4.2-3ubuntu3.1shell with lots of features

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