Software

OS

Ubuntu 24.04 LTS (Noble Numbat)

System Library

/usr/bin, /bin

• Shells
  • bash 5.2.21
  • zsh 5.9
  • tmux: 3.4
• Editors
  • emacs 27.1
  • vim 9.1
  • nano 7.2
• Compilers and interpreters
  • gcc 13.3
  • clang 18.1
  • rustc 1.89
  • python3 3.12
  • ruby 3.2
  • R 4.5
• Other tools
  • git 2.43.0
  • cmake 3.28.3

Some tools are available in newer version. See below.

Job Management System

Slurm 23.11.4

See usage#slurm-workload-manager.

Additional Tools

Additional tools are installed with Homebrew to /home/linuxbrew/.linuxbrew/ if available. Otherwise, they are manually installed to /home/antares/. The environment variable PATH for their bins is preset for all users.

Compilers, Interpreters, and Libraries

• gcc 15.1
• python 3.13
• boost 1.89
• eigen 3.4.0
• gsl 2.8

General tools

• tmux 3.5a
• cmake 4.1.1

Bioinformatics tools

• bcftools 1.22
• bedtools 2.31
• blast 2.16
• bowtie2 2.5.4
• bwa 0.7.19
• diamond 2.1.13
• fastp 1.0.1
• gatk 4.6.0
• hisat2 2.2.1
• hmmer 3.4
• htslib/samtools 1.22
• IQ-TREE 2.3.6, 3.0.1
• lastz 1.04.52
• libsequence 1.9.8
• mafft 7.526
• multiz 20240016
• paml 4.9j
• PLINK 2.0 alpha 6.24
• PHAST v1.8.1
• RAxML-NG 1.2.2
• SeqKit 2.10.1
• SnpEff 4.3
• sratoolkit 3.2.1
• STAR 2.7.11
• stringtie 3.0.1
• trimAl 1.5.0
• varscan 2.4.4
• velvet 1.2.10

/home/antares/sif/bin

• MEME 5.5.5
• OrthoFinder 2.5.5
• Dfam TETools 1.94
  • RepeatMasker 4.2.1
  • RepeatModeler 2.0.7
  • Dfam 3.9 (see famdb.py info)
  • TRF 4.09.1
• salmon 1.10.3
• Trinity 2.15.1

/home/antares/bin

• uv
• ms
• RSEM 1.3.3
• signalp 5.0b
• tmhmm 2.0c

Python

• /usr/bin/python3@ -> python3.12
• /usr/bin/python3.12

The system does not provide any package globally according to PEP 668. You can install packages to your local environment with venv.

You can use uv to install and manage multiple Python versions in your home directory.

uv --help
uv python install 3.13
uv python list
uv venv
source .venv/bin/activate
uv pip install seaborn

R packages

Create your own library directory ~/.R/library/4.5 to install.packages() or pak::pak().

mkdir -p ~/.R/library/4.5
R
# install.packages("cubelyr")

Some popular packages are pre-installed in /home/antares/.R/library/%v and available for all users:

• ape
• BioConductor (Biostrings, GenomicRanges, etc.)
• brms, rstanarm
• cmdstanr, bayesplot
• cowplot
• cpp11, Rcpp
• devtools
• fs
• igraph
• lme4
• pak
• rgl
• rmarkdown
• Seurat
• tidyverse (ggplot2, dplyr, tidyr, etc.)