OS

Ubuntu 22.04 LTS (Jammy Jellyfish)

System Library

/usr/bin, /bin

• Shells
  • bash 5.1.16
  • zsh 5.8.1
• Editors
  • emacs 27.1
  • vim 8.2
  • nano 6.2
• Compilers and interpreters
  • gcc 11.4.0, 12.3.0
  • clang 14.0
  • rustc 1.66.1
  • python3 3.10.12
  • ruby 3.0
  • R 4.3.1
• Other tools
  • git 2.34.1
  • cmake 3.22.1

Some tools are available in newer version. See below.

Job Management System

/opt/pbs

OpenPBS 22.0

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 13.2
• python 3.12
• boost 1.85
• eigen 3.4.0
• gsl 2.7.1

General tools

• tmux 3.4
• cmake 3.29
• git 2.45

Bioinformatics tools

• bcftools 1.20
• bedtools 2.31
• blast 2.15
• bowtie2 2.5.3
• bwa 0.7.18
• fastp 0.23.4
• gatk 4.3.0
• hisat2 2.2.1
• hmmer 3.4
• htslib/samtools 1.20
• lastz 1.04.22
• libsequence 1.9.8
• mafft 7.526
• multiz 20191003
• paml 4.9j
• PLINK v1.90b5
• PHAST v1.6
• RAxML 8.2.12
• SeqKit 2.8.1
• SnpEff 4.3
• sratoolkit 3.1.0
• STAR 2.7.10
• stringtie 2.1.4
• 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@ -> python3.10
• /usr/bin/python3.10
• /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
• cmdstanr
• cowplot
• igraph
• lme4
• Rcpp
• rgl
• rmarkdown
• rstanarm
• Seurat
• tidyverse (ggplot2, dplyr, tidyr, etc.)