taf-compleasm

TAFFISH wrapper for Compleasm, a fast genome and protein completeness assessment tool based on BUSCO marker genes, miniprot, and HMMER.

This repository packages Compleasm 0.2.7 as a TAFFISH tool app. The container installs the Bioconda Compleasm package and exposes the upstream compleasm command together with its runtime tools, including miniprot, hmmsearch, and run_sepp.py.

Installation

Install from the public TAFFISH Hub index:

taf update
taf install compleasm

Install the exact release:

taf install compleasm 0.2.7-r2

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

taf install --from .

Usage

Show TAFFISH app help:

taf-compleasm --help

Show the TAFFISH package version:

taf-compleasm --version

Show the upstream Compleasm version:

taf-compleasm compleasm --version
taf-compleasm -- --version

Show upstream Compleasm help:

taf-compleasm compleasm --help
taf-compleasm -- --help

Official Guide Mapping

The upstream quick-start commands use compleasm_kit/compleasm.py. In this TAFFISH app, the equivalent upstream executable is available as compleasm inside the container, so use taf-compleasm compleasm ...:

# upstream:
# compleasm_kit/compleasm.py download primates
taf-compleasm compleasm download primates

# upstream:
# compleasm_kit/compleasm.py run -t16 -l primates -a hg38.fa -o hg38-mb
taf-compleasm compleasm run -t 16 -l primates -a hg38.fa -o hg38-mb

# upstream autolineage mode, requiring SEPP:
# compleasm_kit/compleasm.py run --autolineage -a hg38.fa -o hs38-mb
taf-compleasm compleasm run --autolineage -a hg38.fa -o hs38-mb

The container already includes pandas, miniprot, hmmsearch, and run_sepp.py, so users do not need to run pip install pandas or conda install sepp inside the container.

Compleasm 0.2.7 uses BUSCO ODB12 by default and is not compatible with ODB10 lineage datasets. Use ODB12 lineage downloads unless you intentionally build a separate older Compleasm release for ODB10.

Compleasm has subcommands such as run, analyze, download, list, miniprot, and protein. Because this is a command-mode TAFFISH tool, the clearest form is to name the upstream command explicitly:

taf-compleasm compleasm run -a genome.fa -o compleasm-out -l eukaryota -t 8
taf-compleasm compleasm protein -p proteins.faa -l eukaryota -o protein-out -t 8
taf-compleasm compleasm list --local -L mb_downloads

Do not use taf-compleasm run ... or taf-compleasm -- run ... for the Compleasm run subcommand. In TAFFISH command mode, the first non-option argument is treated as an in-container executable name. This means taf-compleasm miniprot --version runs the standalone miniprot executable, while taf-compleasm compleasm miniprot ... runs the Compleasm miniprot subcommand.

Download a BUSCO lineage dataset:

taf-compleasm compleasm download eukaryota -L mb_downloads

Run with a specified lineage:

taf-compleasm compleasm run \
  -a genome.fa \
  -o compleasm-out \
  -l eukaryota \
  -L mb_downloads \
  -t 8

Run the miniprot-only submodule without downloading lineage data:

taf-compleasm compleasm miniprot -a genome.fa -p proteins.faa -o miniprot-out -t 8

Access bundled helper executables directly:

taf-compleasm miniprot --version
taf-compleasm hmmsearch -h
taf-compleasm run_sepp.py -h

Package

name: compleasm
command: taf-compleasm
version: 0.2.7-r2
kind: tool
image: ghcr.io/taffish/compleasm:0.2.7-r2

Container

The container image is built from docker/Dockerfile. It starts from mambaorg/micromamba:1.5.10-bookworm-slim and installs a pinned Bioconda environment:

compleasm 0.2.7
miniprot 0.18
hmmer 3.1b2
sepp 4.5.1
dendropy 4.5.2
pandas 1.3.5
python 3.7

The image includes these user-facing commands:

compleasm
miniprot
hmmsearch
run_sepp.py
python

The current release is built for:

linux/amd64

The official Compleasm release asset is x64 Linux, and the full Bioconda environment for Compleasm 0.2.7 currently resolves cleanly on linux/amd64. On linux/arm64, the available sepp packages require a newer DendroPy than Compleasm 0.2.7 allows, so this TAFFISH release keeps full upstream functionality and declares amd64 only.

For Docker and Podman, src/main.taf declares --platform linux/amd64, so arm64 machines such as Apple Silicon Macs can still use the image through normal Docker/Podman amd64 emulation:

TAFFISH_CONTAINER_BACKEND=docker \
  taf-compleasm compleasm --version

TAFFISH_CONTAINER_BACKEND=docker \
  taf-compleasm compleasm run -a genome.fa -o compleasm-out -l eukaryota -t 8

This does not mean the image contains a native arm64 build; it runs the amd64 image through emulation. Apptainer compatibility depends on the host and site configuration.

Smoke Checks

The TAFFISH metadata declares a Docker smoke check:

exist: compleasm, miniprot, hmmsearch, run_sepp.py, python
test:  Compleasm reports upstream version 0.2.7
test:  core Compleasm help and all six subcommand help pages are available
test:  miniprot, hmmsearch, and run_sepp.py are available
test:  Python can import pandas, dendropy, and compleasm
test:  a tiny local protein-to-genome miniprot workflow creates a GFF output

The smoke check covers all Compleasm command surfaces, but it does not download BUSCO lineage datasets. Commands such as download, list --remote, run with a missing lineage, and --autolineage can require network access and external lineage data.

Upstream

• Project: Compleasm
• Repository: https://github.com/huangnengCSU/compleasm
• Release: https://github.com/huangnengCSU/compleasm/releases/tag/v0.2.7
• Upstream license: Apache-2.0, with BUSCO-derived license terms noted by the upstream LICENSE-BUSCO file
• Primary citation: Huang and Li 2023, doi:10.1093/bioinformatics/btad595, PMID:37758247

Maintainer Notes

Useful checks before publishing:

taf check
taf build
taf publish --release --dry-run
docker build --platform linux/amd64 -t ghcr.io/taffish/compleasm:0.2.7-r2 -f docker/Dockerfile .
docker run --rm ghcr.io/taffish/compleasm:0.2.7-r2 compleasm --version
docker run --rm ghcr.io/taffish/compleasm:0.2.7-r2 compleasm --help

The repository wrapper files are licensed under Apache-2.0. Upstream Compleasm is distributed under Apache-2.0 with additional BUSCO-derived license terms, and third-party runtime components are distributed under their own upstream licenses.