Sign inSign up

poeli/gottcha2

By poeli

•Updated 15 days ago

Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) v2 is a signature-based metagenomic profiler.

Image
0

2.6K

poeli/gottcha2 repository overview

⁠GOTTCHA2 Docker Guide

This guide explains how to run GOTTCHA2 using Docker.

⁠Quick Start

⁠Test the Installation
docker run --rm poeli/gottcha2:latest gottcha2 --help
⁠Basic Usage

Run GOTTCHA2 with your data by mounting volumes:

docker run --rm \
  -v /path/to/database:/db:ro \
  -v /path/to/reads:/reads:ro \
  -v /path/to/output:/output \
  poeli/gottcha2:latest \
  gottcha2 profile \
    -d /db/gottcha_db.species.fna \
    -i /reads/sample.fastq \
    -o /output \
    -t 4

Volume mappings:

  • /db - Database directory (read-only recommended)
  • /reads - Input FASTQ/FASTA files (read-only recommended)
  • /output - Output directory for results (read-write)

⁠Common Use Cases

⁠Profile Single-End Reads
docker run --rm \
  -v $(pwd)/database:/db:ro \
  -v $(pwd)/data:/data \
  poeli/gottcha2:latest \
  gottcha2 profile \
    -d /db/RefSeq-r220_BAVxH-cg/gottcha_db.species.fna \
    -i /data/sample.fastq \
    -o /data/results \
    -t 8
⁠Profile with SAM Input

If you already have aligned reads in SAM format:

docker run --rm \
  -v $(pwd)/database:/db:ro \
  -v $(pwd)/data:/data \
  poeli/gottcha2:latest \
  gottcha2 profile \
    -s /data/aligned.sam \
    -d /db/gottcha_db.species.fna \
    -o /data/results
⁠Nanopore Reads

For Nanopore long reads, use the -np flag:

docker run --rm \
  -v $(pwd)/database:/db:ro \
  -v $(pwd)/data:/data \
  poeli/gottcha2:latest \
  gottcha2 profile \
    -d /db/gottcha_db.species.fna \
    -i /data/nanopore.fastq \
    -o /data/results \
    -np \
    -t 8
⁠Extract Reads for Specific Taxa
docker run --rm \
  -v $(pwd)/database:/db:ro \
  -v $(pwd)/data:/data \
  poeli/gottcha2:latest \
  gottcha2 profile \
    -s /data/aligned.sam \
    -d /db/gottcha_db.species.fna \
    -e 562,1280 \
    -o /data/results

⁠Advanced Configuration

⁠Custom Output Formats

Generate results in different formats:

# CSV format
docker run --rm -v $(pwd):/data poeli/gottcha2:latest \
  gottcha2 profile -d /data/db.fna -i /data/reads.fq -fm csv

# BIOM format
docker run --rm -v $(pwd):/data poeli/gottcha2:latest \
  gottcha2 profile -d /data/db.fna -i /data/reads.fq -fm biom
⁠Resource Limits

Limit CPU and memory usage:

docker run --rm \
  --cpus=4 \
  --memory=8g \
  -v $(pwd):/data \
  poeli/gottcha2:latest \
  gottcha2 profile -d /data/db.fna -i /data/reads.fq -t 4
⁠Interactive Shell

Access the container interactively:

docker run --rm -it \
  -v $(pwd):/data \
  --entrypoint /bin/bash \
  poeli/gottcha2:latest

⁠Docker Compose

Create a docker-compose.yml for easier management:

version: '3.8'

services:
  gottcha2:
    image: poeli/gottcha2:latest
    build: .
    volumes:
      - ./database:/db:ro
      - ./input:/input:ro
      - ./output:/output
    command: >
      gottcha2 profile
      -d /db/gottcha_db.species.fna
      -i /input/sample.fastq
      -o /output
      -t 8

Run with:

docker-compose up

⁠Troubleshooting

⁠Check GOTTCHA2 Version
docker run --rm poeli/gottcha2:latest gottcha2 version
⁠Verify Dependencies

Check that minimap2 and samtools are available:

docker run --rm poeli/gottcha2:latest minimap2 --version
docker run --rm poeli/gottcha2:latest samtools --version
⁠Permission Issues

If you encounter permission errors with output files, ensure the output directory has proper permissions or run with user mapping:

docker run --rm \
  --user $(id -u):$(id -g) \
  -v $(pwd):/data \
  poeli/gottcha2:latest \
  gottcha2 profile -d /data/db.fna -i /data/reads.fq -o /data/out

⁠Image Information

  • Base Image: mambaorg/micromamba:1.5-jammy
  • Python Version: 3.8+
  • Key Dependencies: minimap2 ≥2.17, pandas, numpy, biom-format, samtools
  • Working Directory: /data

⁠Support

For issues specific to Docker deployment, please check:

Tag summary

Content type

Image

Digest

sha256:dabf89f32…

Size

438.8 MB

Last updated

15 days ago

docker pull poeli/gottcha2