Containers

Containers and versions / 컨테이너와 버전

QIIME 2

Supported/tested environment: QIIME 2 Amplicon 2025.7, with QIIME 2, q2cli and feature-classifier 2025.7.0. Versions were read with qiime info inside the configured SIF. Normalization, artifact import/validation, visualization and postprocessing have been exercised; a complete QIIME BLAST search is not part of the workflow tests. Other QIIME releases have not been verified.

The local QIIME SIF was built from quay.io/qiime2/amplicon:2025.7. Download it rather than committing a large binary:

mkdir -p containers
singularity pull containers/qiime2_amplicon_2025.7.sif docker://quay.io/qiime2/amplicon:2025.7
nextflow -C nextflow.config run main.nf -profile test \
  --qiime_sif "$PWD/containers/qiime2_amplicon_2025.7.sif"

Official reference: QIIME 2 container guidance.

Native BLAST runtime

The native backend uses a custom image. Its embedded build recipe is preserved at containers/blast_taxonomy.def. It includes Python 3.10, BLAST 2.16.0, TaxonKit 0.18.0, csvtk 0.30.0, pandas 2.2.3, NumPy 1.26.4 and PyYAML 6.0.2.

On a system with Singularity build privileges (or an appropriately configured fakeroot builder):

sudo singularity build containers/blast_taxonomy.sif containers/blast_taxonomy.def

Pass --blast_taxonomy_sif /absolute/path/to/blast_taxonomy.sif for native runs. The definition was extracted from the existing working image; a fresh build has not been tested here, and dependency solving may vary over time. BLAST databases and NCBI taxdump are separate inputs and are not included in this image.

What to distribute

Commit the source, test fixtures, configuration and build definition. *.sif remains ignored by Git. The official QIIME image can be downloaded; native users need either the recipe and build access or a separately hosted prebuilt image. A recipe reproduces the declared environment, not a byte-identical SIF. For exact binary reuse, publish a versioned SIF with a checksum via a registry or suitable artifact storage. No image upload has been performed.

한국어

지원·검증 기준은 QIIME 2 Amplicon 2025.7 / QIIME 2·q2cli·feature-classifier 2025.7.0입니다. 다른 버전의 호환성은 아직 확인하지 않았습니다.
QIIME SIF는 위 공식 이미지에서 다운로드할 수 있으므로 Git에 함께 올릴 필요가 없습니다.
Native BLAST는 직접 만든 이미지이므로 빌드 정의 또는 별도 이미지 배포 경로가 필요합니다. 기존 이미지에서 추출한 containers/blast_taxonomy.def를 포함했습니다.
빌드는 Singularity 빌드 권한이 있는 환경에서 수행하세요. 이번 변경에서 이미지를 새로 빌드하지는 않았으며, 정의 파일만으로 기존 SIF와 바이트 단위 동일성을 보장하지는 않습니다.
BLAST DB와 taxdump는 별도로 준비해야 합니다. SIF 업로드는 수행하지 않았습니다.