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These tools are designed to be simple, efficient, and composable with standard Unix workflows.\n\n## Quick Start\n\n```bash\n# Clone repository\ngit clone https://github.com/olympus-terminal/tools.git\ncd tools\n\n# Make scripts executable\nchmod +x *.sh *.py *.pl\n\n# Add to PATH (optional)\nexport PATH=\"$PATH:$(pwd)\"\n```\n\n## Tool Categories\n\n### Data Processing\n\n**break-to-100s.py** - Split data into chunks of 100 entries\n```bash\npython break-to-100s.py large_dataset.txt\n```\n\n**delim_to_tab_UTF8** - Convert any delimiter to tab-separated values\n```bash\n./delim_to_tab_UTF8 \u003c data.csv \u003e data.tsv\n```\n\n**only_alpha** - Extract only alphabetic characters from input\n```bash\n./only_alpha \u003c mixed_text.txt \u003e letters_only.txt\n```\n\n**get_IDs** - Extract IDs from formatted text\n```bash\n./get_IDs input_file.txt \u003e ids.txt\n```\n\n### File Management\n\n**move_large_files.sh** - Efficiently move large files with progress\n```bash\n./move_large_files.sh /source/dir /dest/dir \"*.bam\"\n```\n\n**osxrename.pl** - Perl-based batch file renaming (macOS compatible)\n```bash\n./osxrename.pl 's/old_pattern/new_pattern/g' *.txt\n```\n\n**filter_ckpts.sh** - Filter and manage checkpoint files\n```bash\n./filter_ckpts.sh checkpoints/ --keep-every 10\n```\n\n**opposite_day.sh** - Reverse file selection logic\n```bash\n./opposite_day.sh pattern files/\n```\n\n### Text \u0026 Document Processing\n\n**pdf_to_txt_argv.py** - Convert PDF files to plain text\n```bash\npython pdf_to_txt_argv.py document.pdf output.txt\n```\n\n**mp3xtractr.py** - Extract metadata from MP3 files\n```bash\npython mp3xtractr.py music_library/ \u003e metadata.csv\n```\n\n**neural_tts.py** - Text-to-speech synthesis utility\n```bash\npython neural_tts.py \"Text to convert to speech\" output.wav\n```\n\n### System Administration\n\n**CatchAndSlot.sh** - Execute commands with proper error handling\n```bash\n./CatchAndSlot.sh long_running_command\n```\n\n**distribute_ex.sh** - Distribute files across multiple systems\n```bash\n./distribute_ex.sh file_list.txt server1 server2 server3\n```\n\n**clone_imprint_distribute** - Clone and distribute configurations\n```bash\n./clone_imprint_distribute template/ target_systems.txt\n```\n\n**download-update.sh** - Automated download and update script\n```bash\n./download-update.sh package_name\n```\n\n### Archive \u0026 Compression\n\n**extract_zip_having_dups.sh** - Extract ZIP files with duplicate handling\n```bash\n./extract_zip_having_dups.sh archive.zip output_dir/\n```\n\n**force_unzip.sh** - Force extraction of damaged archives\n```bash\n./force_unzip.sh corrupted.zip output_dir/\n```\n\n### Data Transfer \u0026 Sync\n\n**optimized_rsync.sh** - Rsync wrapper with optimization\n```bash\n./optimized_rsync.sh /source/dir/ user@host:/dest/dir/\n```\n\n### Bioinformatics\n\n**getFromNCBI-gene.py** - Fetch gene data from NCBI\n```bash\npython getFromNCBI-gene.py gene_list.txt \u003e gene_data.txt\n```\n\n**cid_make_unitigs** - Process unitigs from assembly\n```bash\n./cid_make_unitigs assembly.fa \u003e unitigs.fa\n```\n\n**interleave.sh** - Interleave paired-end sequencing reads\n```bash\n./interleave.sh reads_R1.fq reads_R2.fq \u003e interleaved.fq\n```\n\n**combine-ig-headers.sh** - Combine immunoglobulin sequence headers\n```bash\n./combine-ig-headers.sh sequences.fa \u003e combined.fa\n```\n\n### String Processing\n\n**awktag.sh** - AWK-based string tagging\n```bash\n./awktag.sh pattern input.txt\n```\n\n**betterthanbasename** - Enhanced basename functionality\n```bash\n./betterthanbasename /path/to/file.tar.gz .tar.gz\n```\n\n## Usage Examples\n\n### Pipeline Processing\n```bash\n# Convert CSV to TSV, extract IDs, process in chunks\ncat data.csv | \\\n  ./delim_to_tab_UTF8 | \\\n  ./get_IDs | \\\n  python break-to-100s.py\n```\n\n### Bulk File Operations\n```bash\n# Rename all files matching pattern\n./osxrename.pl 's/IMG_/photo_/g' *.jpg\n\n# Move large files with progress\n./move_large_files.sh raw_data/ processed_data/ \"*.fastq.gz\"\n```\n\n### System Management\n```bash\n# Distribute configuration to multiple servers\n./distribute_ex.sh config_files.txt web1 web2 web3\n\n# Execute with error handling\n./CatchAndSlot.sh ./critical_backup.sh\n```\n\n## Requirements\n\nMost tools require only standard Unix utilities. Specific requirements:\n\n- **Python scripts**: Python 3.6+\n- **Perl scripts**: Perl 5.10+\n- **C programs**: Compile with `gcc only_alpha.c -o only_alpha`\n\nPython dependencies (if needed):\n```bash\npip install beautifulsoup4 requests pdftotext\n```\n\n## Installation\n\n```bash\n# Clone repository\ngit clone https://github.com/olympus-terminal/tools.git\ncd tools\n\n# Make all scripts executable\nfind . -name \"*.sh\" -o -name \"*.py\" -o -name \"*.pl\" | xargs chmod +x\n\n# Compile C programs\ngcc only_alpha.c -o only_alpha\n\n# Add to PATH\necho 'export PATH=\"$PATH:'$(pwd)'\"' \u003e\u003e ~/.bashrc\nsource ~/.bashrc\n```\n\n## Contributing\n\nContributions welcome. Please:\n1. Fork the repository\n2. Create a feature branch\n3. Add your tool with usage documentation\n4. Submit a pull request\n\n## License\n\nMIT License - see [LICENSE](LICENSE) file for details.\n\n## Contact\n\n- Issues: [GitHub Issues](https://github.com/olympus-terminal/tools/issues)\n- Author: [@olympus-terminal](https://github.com/olympus-terminal)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Folympus-terminal%2Funix-utilities","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Folympus-terminal%2Funix-utilities","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Folympus-terminal%2Funix-utilities/lists"}