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
/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 bin
s 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.)