README FOR public_download/install_bioinformatics-tools.sh

Purpose
This folder contains `install_bioinformatics-tools.sh`, a public helper script for installing a collection of third-party open-source bioinformatics, molecular modeling, and supporting build tools on Ubuntu Linux.

This public installer is independent of AstraBioSuite application setup. It installs supported third-party tools, but it does not create AstraBioSuite config files, does not write `~/.config/AstraBioSuite/bioinformatics-tools_paths.json`, and does not modify shell startup files such as `~/.bashrc`.

Recommended Platform
- Ubuntu 24.04 LTS (recommended)
- Bash shell
- Regular user account with `sudo` privileges
- Internet access for downloads from Ubuntu repositories and public upstream sources

Core Requirements
- `cmake`
  Recommended: CMake 3.28 or newer
  The script can install a private newer CMake under the tool root if the system version is too old.
- `build-essential`
- `ninja-build`
- `pkg-config`
- `gfortran`
- `git`
- `curl`
- `wget`
- `tar`
- `python3`
- `python3-pip`
- `python3-venv`
- `python3-dev`
- `sudo`

Software Installed by This Script
- GROMACS 2025.4
- CMake 3.28 or newer when needed
- Micromamba
- ACPYPE / AmberTools
- MGLTools 1.5.6
- LightDock
- OpenMM 8.2.0
- PDBFixer 1.12
- MDAnalysis
- gmx_MMPBSA 1.6.4
- Packmol
- Open Babel
- AutoDock Vina
- FFmpeg

Default Installation Location
- Third-party tools are installed under:
  `~/bioinformatics-tools`
- Logs are written under:
  `~/bioinformatics-tools/logs`

Important Behavior
- Run the script as a normal user, not as `root`.
- The script uses `sudo` for system package installation.
- The script may install CPU-only or CUDA-enabled GROMACS depending on detected hardware and user confirmation.
- The script prompts for acceptance of the disclaimer before installation proceeds.
- The full disclaimer text is also provided in `DISCLAIMER.txt`.

How To Run
1. Open a terminal in this folder.
2. Make the script executable if needed:
   `chmod +x install_bioinformatics-tools.sh`
3. Run:
   `./install_bioinformatics-tools.sh`

Ownership, Distribution, and Liability
SiBioLEAD does not claim ownership of this installer as a packaged software product, and does not claim ownership of any third-party software installed by this script.

SiBioLEAD does not distribute, relicense, or represent itself as the owner of GROMACS, MGLTools, OpenMM, PDBFixer, gmx_MMPBSA, ACPYPE, LightDock, MDAnalysis, AutoDock Vina, Open Babel, Packmol, FFmpeg, AmberTools, CUDA Toolkit, micromamba, or any other upstream project referenced by this installer. Each software package remains subject to its own license, notice, citation, and usage terms.

This script is provided free of charge as a public convenience and is offered "as is", without warranty of any kind, whether express or implied.

You install and use these tools at your own discretion and risk. You are responsible for reviewing the licenses, notices, documentation, and citation requirements of each upstream software package, and for determining whether the software is suitable for your own research, academic, commercial, clinical, regulatory, security, or production use.

SiBioLEAD is not liable for installation failures, data loss, software defects, system misconfiguration, incompatibilities, security issues, licensing issues, downtime, or any direct or indirect damages arising from use of this script or the third-party software it installs.

If you do not accept these terms, do not run the script.
