This directory contains Dockerfiles for all bioinformatics tools used in the DeepCritical project. Each Dockerfile is optimized for the specific tool and includes all necessary dependencies.

# Build a specific tool container
docker build -f docker/bioinformatics/Dockerfile.bcftools -t deepcritical-bcftools:latest .

# Build all containers
for dockerfile in docker/bioinformatics/Dockerfile.*; do
    tool=$(basename "$dockerfile" | cut -d'.' -f2)
    docker build -f "$dockerfile" -t "deepcritical-${tool}:latest" .
done

# Run BCFtools container
docker run --rm -v $(pwd):/data deepcritical-bcftools:latest bcftools view -h /data/sample.vcf

# Run with interactive shell
docker run --rm -it -v $(pwd):/workspace deepcritical-bcftools:latest /bin/bash

from DeepResearch.src.tools.bioinformatics.bcftools_server import BCFtoolsServer

# Create server instance
server = BCFtoolsServer()

# Deploy with Docker
deployment = await server.deploy_with_testcontainers()
print(f"Container ID: {deployment.container_id}")

Each Dockerfile includes:

• Base Image: Python 3.11-slim for consistency
• System Dependencies: All required libraries and tools
• Python Dependencies: Tool-specific Python packages
• Health Checks: Container health monitoring
• Environment Variables: Tool-specific configuration
• Working Directory: Consistent /workspace setup

All containers include health checks and can be tested using:

# Test container health
docker run --rm deepcritical-bcftools:latest bcftools --version

# Run bioinformatics tests
make test-bioinformatics

• Compression: zlib, libbz2, liblzma
• Bioinformatics: htslib (samtools, bcftools)
• Java: OpenJDK 11 (FastQC, Picard, Qualimap)
• R: R-base (Qualimap)
• Perl: Perl libraries (HOMER, MEME)

• Core: numpy, scipy, matplotlib
• Bioinformatics: pysam, biopython
• Specialized: cutadapt, deeptools, HTSeq, etc.

• All containers use multi-stage builds where applicable
• Health checks prevent running failed containers
• Minimal base images reduce attack surface
• Proper dependency management ensures reproducibility
• Volume mounting support for data persistence

1. Permission Denied: Ensure Docker daemon is running and user has permissions
2. Port Conflicts: Use different ports or check existing containers
3. Memory Issues: Increase Docker memory limits for large datasets
4. Network Issues: Check firewall settings and network configuration

# Check container logs
docker logs <container_id>

# Inspect container
docker inspect <container_id>

# Enter running container
docker exec -it <container_id> /bin/bash

When adding new bioinformatics tools:

1. Create a new Dockerfile following the established pattern
2. Add appropriate tests in tests/test_bioinformatics_tools/
3. Update this README with tool information
4. Test the container thoroughly before deployment

These Dockerfiles are part of the DeepCritical project and follow the same licensing terms.

[69 tools called]

Dockerfiles created for:

• bcftools
• bedtools
• bowtie2
• busco
• bwa
• cutadapt
• deeptools
• fastp
• fastqc
• featurecounts
• flye
• freebayes
• hisat2
• homer
• htseq
• kallisto
• macs3
• meme
• minimap2
• multiqc
• picard
• qualimap
• salmon
• samtools
• seqtk
• star
• stringtie
• tophat
• trimgalore

Key features of each Dockerfile:

• Python 3.11-slim base image for consistency
• All required system dependencies pre-installed
• Tool-specific Python packages
• Health checks for container monitoring
• Proper environment variable configuration
• Working directory setup

test files for:

• bcftools_server
• bowtie2_server
• busco_server
• cutadapt_server
• deeptools_server
• fastp_server
• fastqc_server
• flye_server
• homer_server
• htseq_server
• kallisto_server
• macs3_server
• meme_server
• minimap2_server
• multiqc_server
• picard_server
• qualimap_server
• salmon_server
• seqtk_server
• stringtie_server
• tophat_server
• trimgalore_server

Test structure follows existing patterns:

• Inherits from BaseBioinformaticsToolTest
• Includes sample data fixtures
• Tests basic functionality, parameter validation, and error handling
• All marked with @pytest.mark.optional for proper test organization

1. Build containers:

   docker build -f docker/bioinformatics/Dockerfile.bcftools -t deepcritical-bcftools:latest .

2. Run bioinformatics tests:

   make test-bioinformatics

3. Use in bioinformatics workflows:

   from DeepResearch.src.tools.bioinformatics.bcftools_server import BCFtoolsServer
   server = BCFtoolsServer()
   deployment = await server.deploy_with_testcontainers()

The implementation provides a complete containerized environment for all bioinformatics tools used in DeepCritical, ensuring reproducibility and easy deployment across different environments.