Bioutils

A personal collection of standalone, portable command-line utilities for bioinformatics and data analysis.

Categories

• fasta/ - Scripts working with FASTA sequence files
• fastq/ - Scripts working with FASTQ files
• file_formats/ - Scripts modifying or converting file formats

More information on each script given in the README file in each folder.

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Installation

Option 1: Install all scripts

Clone the repository and run the installer:

git clone https://github.com/sverwimp/portable-bioinformatics-scripts.git
cd portable-bioinformatics-scripts
chmod +x install.sh
./install.sh

This will:

• Install all scripts to ~/.bioutils (or a custom directory of your choice)
• Make all scripts executable
• Compile any C programs automatically (only if gcc and zlib are present)
• Add the directory to your PATH

Custom installation directory:

./install.sh                    # Install to ~/.bioutils
./install.sh ~/myscripts        # Install to ~/myscripts
./install.sh /usr/local/bin     # System-wide (requires sudo)

Use ./install.sh -h for more information

Option 2: Use individual scripts

Each script is self-contained. You can copy any single script directly and use it without installing the entire collection.

Scripts written in C can be compiled as followed: gcc -O2 <scriptname>.c -o <scriptname> -lz

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Management

Once installed, use the bioutils command to manage the collection of scripts.

Usage

bioutils <subcommand>

Subcommand	Description
list	List all available scripts in your installation directory.
info <name>	Show metadata (path, executable status, modified date) for a script.
update	Automatically pull the latest changes from GitHub and reinstall.
remove <name...>	Remove specific script(s) by name.
uninstall-all	Remove all scripts, the directory, and clean up your shell's PATH.

Updating

Use the bioutils update subcommand to automatically clone the repository to a temporary location, run the install script again (keeping current install directory in mind), and remove the local repository.

Or pull new changes manually and simply run the installer again:

git pull
./install.sh <installation_directory>

Only modified or new scripts will be copied. Use ./install.sh -f to force reinstall everything.

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Requirements

All scripts use either standard Unix tools (bash, awk, grep), Python, or C (requires gcc and zlib) and should work on Linux/macOS without additional dependencies.