Table of Contents

Software

This section documents the software available on ABI's computing infrastructure, how to use it, and how to install your own tools.

How Software is Managed

All commonly used bioinformatics tools are installed globally on the cluster and available to all users. There is no module system – simply type the command name to use a tool: 

# Check if a tool is available
which bwa
bwa --version
 
which samtools
samtools --version

If you need software that is not installed, you have two options:

  1. Request system-wide installation – email it-support@abi.am with the tool name and version.
  2. Install locally with Conda – see Installing Software with Conda. Note: do not add Conda to your ~/.bashrc to keep logins fast.

Software by Category

NGS / Genomics Tools

Tool Purpose Version Documentation
BWA Short read alignment *TODO* GitHub
samtools SAM/BAM manipulation *TODO* htslib.org
bcftools Variant calling & VCF manipulation *TODO* docs
GATK Variant discovery *TODO* Broad
FastQC Read quality assessment *TODO* Babraham
MultiQC Aggregate QC reports *TODO* multiqc.info
fastp Read QC and trimming *TODO* GitHub
Bowtie2 Short read alignment *TODO* docs
STAR RNA-seq splice-aware alignment *TODO* GitHub
*TODO* *Add more tools as needed*

Machine Learning & AI

Tool Purpose Version Documentation
Python General purpose / data science *TODO* python.org
TensorFlow Deep learning framework *TODO* tensorflow.org
PyTorch Deep learning framework *TODO* pytorch.org
*TODO* *Add more tools as needed*

Programming Languages & Environments

Tool Purpose Version Documentation
Python Scripting, data analysis, ML *TODO* python.org
R Statistical computing *TODO* r-project.org
Conda/Miniconda Package & environment manager *TODO* conda.io
*TODO* *Add more as needed*

System & Cluster Tools

Tool Purpose Documentation
Slurm Job scheduling & resource management ABI Slurm Guide
SSH Remote access SSH Setup Guide
*TODO* *Add screen, tmux, etc. if available*

Installing Your Own Software

If you need software that is not available system-wide, you can install it yourself using Conda:

Note: do not let Conda add itself to your ~/.bashrc – this slows down SSH logins. See the Conda guide for the recommended setup.

Requesting New Software

To request a tool be installed system-wide for all users:

  1. Email it-support@abi.am with:
    • Tool name and version
    • URL to the tool's homepage or repository
    • Why you need it (brief)
  2. The IT team will evaluate and install it.

See Also