Skip to content

v0.18.0

Choose a tag to compare

View all tags
@github-actions github-actions released this 03 Aug 11:33
· 34 commits to main since this release
v0.18.0
351fd58
This commit was created on GitHub.com and signed with GitHub’s verified signature.
GPG key ID: B5690EEEBB952194
Verified
Learn about vigilant mode.

Highlights

v0.18.0 adds atb agc, a new command group for AllTheBacteria's AGC
(Assembled Genomes Compressor) archives. You can now list, inspect, and extract
assembled genomes, and download them by species or by sample accession, straight
from the terminal. The atb agc group is new in this release; v0.17.x does not
include it.

  • Read AGC archives. atb agc install fetches the upstream agc binary
    (Linux/macOS x64+arm64, Windows x64); atb agc ls lists samples or a sample's
    contigs, atb agc info prints archive metadata, and atb agc get extracts
    FASTA by contig (contig[@sample][:from-to]), by --sample, or the whole
    collection with --all - to stdout or a file (-o), with optional --gzip
    and line wrapping (-l).
  • Download by species. atb agc download --species <name> resolves and
    extracts every .agc batch for a species from AllTheBacteria's OSF storage.
  • Download only the samples you need. Pass atb agc download sample
    accessions (positional, a --from file, or piped stdin) and it resolves each
    to the batch that holds it, downloading only those batches.
  • Locate without downloading. atb agc locate [accession...] reports the
    AGC batch, species, and OSF node for each accession as TSV or --format json,
    fetching nothing.

Batches resolve from a cache-first, md5-verified index over the finalized
balanced v202505 collection across its three public OSF nodes. The combined
index is published for download, and the nodes are crawled and joined
automatically when it is unavailable; atb agc index builds or refreshes it, and
--agc-index <file> reads a local TSV instead.

See the AGC guide for a
full walkthrough.

Install

curl -fsSL https://raw.githubusercontent.com/allthebacteria/atb-cli/main/install.sh | bash

Pre-built binaries for all platforms are on the
releases page.

Full changelog: v0.17.1...v0.18.0

Assets 9
Loading