Installer bioawk avec Homebrew, apt, Nix

Liens du projet

• Page d'accueil
• Docs amont
• Page du gestionnaire de paquets

Commandes et alias

• bioawk

Historique du projet

The lh3/bioawk repository was created on GitHub in January 2012 and describes the project as BWK awk modified for biological data. Its README says bioawk extends Brian Kernighan's awk with BED, GFF, SAM, VCF, FASTA/FASTQ, tab-delimited headers, gzip support through zlib, and biosequence helper functions while falling back to original awk behavior when the biological extensions are not used.

Historique d'adoption

bioawk spread through the practical genomics command-line ecosystem rather than through a large application platform. The input package metadata lists Homebrew, Debian, Ubuntu, and Nix packages, which is exactly the distribution pattern expected for a small Unix filter that bioinformaticians drop into shell pipelines.

Modes d'utilisation

Common uses include extracting fields from VCF or SAM, converting FASTA/FASTQ records, reverse-complementing sequences, and using `-c fastx`, `-c sam`, `-c vcf`, or `-c hdr` to make biological records feel like awk fields.

It is especially useful when the job is too small for a full Python or Perl script but too biological for plain awk.

Pourquoi les passionnés de paquets s'y intéressent

bioawk is package-nerd catnip because it is not a new workflow engine or framework; it is the old Unix text-processing model with just enough domain knowledge to remove glue code. It keeps awk's one-liner culture alive inside genomics pipelines.

Chronologie

• 2012: lh3/bioawk repository created on GitHub.
• 2012: v1.0 tag published in the repository.
• 2010s: Packaged by Unix-like distributions for bioinformatics shell workflows.

Related projects

• bioawk is directly related to BWK awk, zlib, and command-line genomics tools such as samtools, bcftools, BED/GFF utilities, and FASTA/FASTQ pipeline filters.

Sources

• https://api.github.com/repos/lh3/bioawk
• https://github.com/lh3/bioawk
• https://raw.githubusercontent.com/lh3/bioawk/master/README.md
• source_facts.package-manager