Metagenomics_Pipeline_Container

Version: v1
Description: A comprehensive container for metagenomics binning, refinement, taxonomy, and annotation.

Key Features

• All-in-One Pipeline: Integrates MetaWRAP, dRep, GTDB-Tk, CheckM v1, SPAdes, and MicrobeAnnotator.
• Environment Isolation: Solved dependency conflicts using isolated Conda environments for each tool (e.g., Python 2.7 for MetaWRAP, Python 3.x for others).
• Smart Wrappers: No need to run conda activate. All tools (e.g., metawrap, checkm, gtdbtk) are directly executable from /usr/local/bin.
• Patched & Optimized: Includes fixes for MetaWRAP BLAS/MKL conflicts and supports SPAdes v4.2.0 alongside legacy versions.

Database Setup

The container requires external databases mounted to /ref_db. Please organize your host directory strictly as follows:

/your/host/db/path/
├── gtdb/               # GTDB-Tk data (release 207/214)
├── checkm/             # CheckM v1 data
├── microbeannotator/   # MicrobeAnnotator data
└── metawrap/           # MetaWRAP databases (MUST include these subfolders):
      ├── BMTAGGER_DB   # Host contamination removal files
      ├── NCBI_nt       # NCBI Nucleotide database
      └── NCBI_tax      # NCBI Taxonomy database

Quick Start

1. Apptainer / Singularity

General syntax

apptainer exec --bind /your/host/db/path:/ref_db metagenome_v1.sif <tool> [args]

Example: Run MetaWRAP Binning

apptainer exec --bind /data/db:/ref_db metagenome_v1.sif \
    metawrap binning -o out_dir -t 24 -a assembly.fa clean_reads_1.fq clean_reads_2.fq

2. Docker

Note: Mount current directory to /work to save outputs

docker run --rm -v /your/host/db/path:/ref_db -v "$PWD":/work -w /work \
    metagenome:v1 metawrap binning ...

Included Tools & Versions

Tool	Version	Env Python
MetaWRAP	v1.3.2	2.7
dRep	v3.6.2	3.10
GTDB-Tk	v2.2.0	3.8
CheckM	v1.1.3	3.7
SPAdes	v4.2.0	3.10
MicrobeAnnotator	v2.0.5	3.8