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
• lastz 1.04.52
• libsequence 1.9.8
• mafft 7.526
• multiz 20240016
• paml 4.9j
• PLINK 2.0 alpha 6.23
• 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
• RepeatMasker 4.1.5
• salmon 1.10.3
• Trinity 2.15.1

/home/antares/bin

• 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.

R packages

/home/antares/.R/library

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