taf-augustus

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

This repository packages AUGUSTUS as a TAFFISH tool app. The command is exposed as:

taf-augustus

Usage

Show TAFFISH wrapper help:

taf-augustus --help

Pass arguments to 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 is useful when an option such as --help should be passed to the upstream command rather than handled by the TAFFISH wrapper.

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

Upstream

• Project: AUGUSTUS
• Source: https://github.com/Gaius-Augustus/Augustus