taf-augustus

TAFFISH wrapper for AUGUSTUS, a gene prediction tool for eukaryotic genomic sequences.

This repository packages AUGUSTUS as a TAFFISH tool app. It exposes upstream augustus through a versioned TAFFISH command while keeping the runtime environment inside a portable container image.

Installation

Install from the public TAFFISH Hub index:

taf update
taf install augustus

Install the exact release:

taf install augustus 3.5.0-r1

For local testing before the app is published to the public index:

taf install --from .

Usage

Show TAFFISH app help:

taf-augustus --help

Run upstream AUGUSTUS:

taf-augustus -- --help
taf-augustus -- --species=help
taf-augustus -- --species=human genome.fa
taf-augustus -- --species=human --gff3=on genome.fa

The -- separator passes following arguments to upstream augustus instead of the TAFFISH wrapper itself. This is useful for upstream options such as --help.

Because this is a command-mode TAFFISH tool, explicit commands can also be run in the same container image:

taf-augustus augustus --species=help
taf-augustus augustus --species=human genome.fa

Package

name: augustus
command: taf-augustus
version: 3.5.0-r1
kind: tool
image: ghcr.io/taffish/augustus:3.5.0-r1

Container

The container image is built from docker/Dockerfile and installs the Debian packages:

augustus
augustus-data
augustus-doc

AUGUSTUS_CONFIG_PATH is set to:

/usr/share/augustus/config

The TAFFISH metadata declares a Docker smoke check:

exist: augustus
test:  augustus --species=help
test:  augustus --version 2>&1 | grep -F 'AUGUSTUS (3.5.0)' >/dev/null

During TAFFISH Hub indexing, this smoke metadata is used to verify that the published image can be inspected, that the upstream executable is available, that bundled AUGUSTUS species configuration can be read, and that the packaged AUGUSTUS version remains 3.5.0.

Upstream

• Project: AUGUSTUS
• Homepage: https://bioinf.uni-greifswald.de/augustus/
• Source: https://github.com/Gaius-Augustus/Augustus
• Release page: https://github.com/Gaius-Augustus/Augustus/releases

Maintainer Notes

Useful checks before publishing:

taf check
taf compile -- --species=help
taf publish --release --dry-run
docker build --check -f docker/Dockerfile .

The repository wrapper files are licensed under Apache-2.0. AUGUSTUS and the Debian packages installed in the container are distributed under their own upstream licenses.