This directory contains Docker configurations for PyEED's bioinformatics services:

• BLAST for sequence similarity searches
• Clustal Omega for multiple sequence alignment
• MMSeqs2 for fast sequence clustering

1. Install Docker and Docker Compose on your system
2. Clone this repository
3. Navigate to the docker directory
4. Run the services:

docker-compose up -d

The BLAST service requires a local BLAST database. The service mounts the local database directory to the container:

volumes:
  - ./blast:/usr/local/bin/data

1. Place your FASTA sequences in ./blast/test_files/
2. Create BLAST database in ./blast/test_db/:

cd blast/test_db
makeblastdb -in ../test_files/protein_sequences.fasta -dbtype prot -out protein_db

The database files (*.pdb, *.phr, etc.) will be available to the container through the mounted volume.

Clustal Omega service mounts two directories:

volumes:
  - ./clustalo:/app/data   # Input/output data

This allows:

• Persistent storage of alignment results
• Access to input/output files from host system

MMSeqs2 service mounts its directory for code and data:

volumes:
  - ./mmseqs2:/app

This enables:

• Code updates without rebuilding container
• Access to clustering results
• Temporary file management

Docker volumes provide a way to persist data and share files between the host system and containers. In the context of PyEED:

1. Syntax: - ./local/path:/container/path

   • Left side: Path on your host machine
   • Right side: Path inside the container

2. Use Cases:

   • Persisting databases (BLAST)
   • Sharing configuration files

3. Benefits:

   • Data persists between container restarts
   • Easy data backup
   • Direct file access from host
   • Improved development workflow

After starting the services, they are available at:

• BLAST: http://localhost:6001
• Clustal Omega: http://localhost:5001
• MMSeqs2: http://localhost:8001

Each service provides a Swagger UI at /docs for API documentation.

To modify the services:

1. Edit code in the respective service directories
2. Changes are reflected immediately due to volume mounting
3. For dependency changes, rebuild the containers:

docker-compose build
docker-compose up -d

1. Volume Permissions:

   • Ensure proper read/write permissions on mounted directories
   • Fix with: chmod -R 755 ./service_directory

2. Database Access:

   • Verify database files are in correct location
   • Check file permissions
   • Ensure proper volume mounting

3. Port Conflicts:

   • Change ports in docker-compose.yml if needed
   • Check for other services using same ports

version: "2.2"
services:

  clustalo:
    build:
      context: clustalo/
    container_name: clustalo
    ports:
      - "5001:5001"
    volumes:
      - ./clustalo:/app/data

  blast:
    build:
      context: blast/
    container_name: blast
    ports:
      - "6001:6001"
    volumes:
      - /mnt/databases:/databases

  mmseqs:
    build:
      context: mmseqs2/
    container_name: mmseqs
    ports:
      - "8001:8001"
    volumes:
      - ./mmseqs2:/app

To build the services, run:

docker-compose build

To start the services, run:

docker-compose up -d