====== 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:

<code bash>
# Check if a tool is available
which bwa
bwa --version

which samtools
samtools --version
</code>

If you need software that is not installed, you have two options:
  - **Request system-wide installation** -- email [[mailto:it-support@abi.am|it-support@abi.am]] with the tool name and version.
  - **Install locally with Conda** -- see [[software:conda|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 ^
| [[software:bwa|BWA]] | Short read alignment | *TODO* | [[https://github.com/lh3/bwa|GitHub]] |
| [[software:samtools|samtools]] | SAM/BAM manipulation | *TODO* | [[https://www.htslib.org/|htslib.org]] |
| [[software:bcftools|bcftools]] | Variant calling & VCF manipulation | *TODO* | [[https://samtools.github.io/bcftools/|docs]] |
| [[software:gatk|GATK]] | Variant discovery | *TODO* | [[https://gatk.broadinstitute.org/|Broad]] |
| [[software:fastqc|FastQC]] | Read quality assessment | *TODO* | [[https://www.bioinformatics.babraham.ac.uk/projects/fastqc/|Babraham]] |
| [[software:multiqc|MultiQC]] | Aggregate QC reports | *TODO* | [[https://multiqc.info/|multiqc.info]] |
| [[software:fastp|fastp]] | Read QC and trimming | *TODO* | [[https://github.com/OpenGene/fastp|GitHub]] |
| [[software:bowtie2|Bowtie2]] | Short read alignment | *TODO* | [[https://bowtie-bio.sourceforge.net/bowtie2/|docs]] |
| [[software:star|STAR]] | RNA-seq splice-aware alignment | *TODO* | [[https://github.com/alexdobin/STAR|GitHub]] |
| *TODO* | *Add more tools as needed* | | |

==== Machine Learning & AI ====

^ Tool ^ Purpose ^ Version ^ Documentation ^
| [[software:python|Python]] | General purpose / data science | *TODO* | [[https://www.python.org/|python.org]] |
| [[software:tensorflow|TensorFlow]] | Deep learning framework | *TODO* | [[https://www.tensorflow.org/|tensorflow.org]] |
| [[software:pytorch|PyTorch]] | Deep learning framework | *TODO* | [[https://pytorch.org/|pytorch.org]] |
| *TODO* | *Add more tools as needed* | | |

==== Programming Languages & Environments ====

^ Tool ^ Purpose ^ Version ^ Documentation ^
| [[software:python|Python]] | Scripting, data analysis, ML | *TODO* | [[https://www.python.org/|python.org]] |
| [[software:r|R]] | Statistical computing | *TODO* | [[https://www.r-project.org/|r-project.org]] |
| [[software:conda|Conda/Miniconda]] | Package & environment manager | *TODO* | [[https://docs.conda.io/|conda.io]] |
| *TODO* | *Add more as needed* | | |

==== System & Cluster Tools ====

^ Tool ^ Purpose ^ Documentation ^
| [[software:slurm|Slurm]] | Job scheduling & resource management | [[software:slurm|ABI Slurm Guide]] |
| SSH | Remote access | [[getting_started:new_member#step_2_set_up_ssh|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**:

  * **[[software:conda|Installing Software with Conda]]** -- Full guide to setting up Miniconda, creating environments, and installing packages.

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:

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



----

===== See Also =====

  * [[databases:start|Databases & Reference Data]] -- Reference genomes and shared datasets
  * [[pipelines:start|Pipelines]] -- End-to-end bioinformatics workflows using these tools
  * [[scripts:start|Scripts]] -- Reusable scripts for common tasks