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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.:
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export PATH="/stor/system/opt/sratoolkit.2.8.2-ubuntu64/bin:$PATH" |
Programs in /mnt/bioi/tools
All compute servers have a shared, read-only /mnt/bioi directory mounted that contains many useful bioinformatics resources such as annotations and other references in /mnt/bioi/ref_genome and external data in /mnt/bio/data).T
Specifically, the /mnt/bioi/tools directory contains several tool suites and their associated data (e.g. cellranger, GSEA), and each tool suite directory has multiple tool version sub-directories. Like the suites in /stor/system/opt, the associated binaries are not on your PATH by default, but can be added as needed, e.g.:
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export PATH="/mnt/bioi/tools/cellranger/8.0.0/bin":$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:
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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 |
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 |
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| 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/)
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| 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 | 0.7.17-1ubuntu0.1 | 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 |
| 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 |
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-bio | 3.0.1ubuntu1 | Debian Med bioinformatics packages |
| med-cloud | 3.0.1ubuntu1 | Debian Med bioinformatics applications usable in cloud computing |
microbiomeutil | 20101212+dfsg1-1build1 | Microbiome Analysis Utilities |
| minfi | 1.24.0 | 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 |
| Rsubread | 2.4.3 | 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 |
| zsh | 5.4.2-3ubuntu3.1 | shell with lots of features |
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