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Docker Run Command

PROTÉGÉ PD runs in a Docker container with Python 3.10 and includes a minimal interactive web interface built with Dash. Here’s the complete command structure: 
docker run --rm \
  --mount type=bind,source=/your/files/path/,target=/root/. \
  --name protege \
  -p 127.0.0.1:8050:8050 \
  --cpus 4 \
  ddelgadillo/protege_base:v1.0.2 \
  protege-pd -s myseqs.fna

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Command Breakdown

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Container Lifecycle

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--rm
flag
Automatically removes the container when it exits. This ensures no orphaned containers accumulate on your system after each run.
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--name
string
default:"protege"
Assigns a friendly name to the running container for easier reference and management.

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Volume Mounting

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--mount
bind mount
required
Binds your local file system to the container’s file system, allowing PROTÉGÉ to access input files and write output files.Parameters:
  • type=bind - Specifies a bind mount (direct mapping)
  • source=/your/files/path/ - Your local directory containing FASTA files
  • target=/root/. - Container’s working directory where files are accessible
Replace /your/files/path/ with the absolute path to your local directory containing FASTA files. Relative paths may not work correctly.
Example mount points: 
--mount type=bind,source=/home/username/protege-data/,target=/root/.

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Port Mapping

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-p
port mapping
default:"127.0.0.1:8050:8050"
Maps the container’s web interface port to your local machine.Format: host_ip:host_port:container_port
  • 127.0.0.1 - Localhost only (secure, not accessible from network)
  • 8050 (first) - Port on your local machine
  • 8050 (second) - Port inside the container where Dash runs
After running PROTÉGÉ, access the web interface at http://127.0.0.1:8050 in your browser.

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CPU Allocation

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--cpus
integer
default:"4"
Limits the number of CPU cores the container can use. PROTÉGÉ performs sequence alignment and primer design, which benefits from multiple cores.Recommendations:
  • Small datasets (< 50 sequences): 2-4 CPUs
  • Medium datasets (50-200 sequences): 4-8 CPUs
  • Large datasets (> 200 sequences): 8+ CPUs

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Working Directory

The container’s working directory is /root/. All input files specified with -s are relative to this directory, which maps to your mounted source path. Example: 
# If your file is at: /home/user/data/sequences.fna
# And you mount: source=/home/user/data/,target=/root/.
# Then specify: -s sequences.fna

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Common Usage Patterns

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Basic Run (Default Parameters)

docker run --rm \
  --mount type=bind,source=/path/to/data/,target=/root/. \
  --name protege \
  -p 127.0.0.1:8050:8050 \
  --cpus 4 \
  ddelgadillo/protege_base:v1.0.2 \
  protege-pd -s genes.fasta

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Custom Consensus Threshold

docker run --rm \
  --mount type=bind,source=/path/to/data/,target=/root/. \
  --name protege \
  -p 127.0.0.1:8050:8050 \
  --cpus 4 \
  ddelgadillo/protege_base:v1.0.2 \
  protege-pd -s genes.fasta -c 85
This sets consensus percentage to 85% instead of the default 90%.

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Longer Primers with Verbose Output

docker run --rm \
  --mount type=bind,source=/path/to/data/,target=/root/. \
  --name protege \
  -p 127.0.0.1:8050:8050 \
  --cpus 8 \
  ddelgadillo/protege_base:v1.0.2 \
  protege-pd -s genes.fasta -d 10 -v
Uses 10-codon primers (30 nucleotides) and enables verbose logging.

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Disable Gap Consensus

docker run --rm \
  --mount type=bind,source=/path/to/data/,target=/root/. \
  --name protege \
  -p 127.0.0.1:8050:8050 \
  --cpus 4 \
  ddelgadillo/protege_base:v1.0.2 \
  protege-pd -s genes.fasta -g
The -g flag disables gap consideration in consensus calculations. Positions with gaps will be excluded.

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Viewing Help

docker run --rm \
  --mount type=bind,source=.,target=/root/. \
  --name protege \
  -p 127.0.0.1:8050:8050 \
  --cpus 4 \
  ddelgadillo/protege_base:v1.0.2 \
  protege-pd --help

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Accessing the Web Interface

Once PROTÉGÉ starts processing:
  1. Watch the terminal for processing messages
  2. When you see “Dash is running on http://0.0.0.0:8050/”
  3. Open your browser to http://127.0.0.1:8050
  4. The interactive primer visualization interface will load
The web interface provides interactive visualizations of primer candidates and allows you to download results.

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Stopping PROTÉGÉ

To stop the running container:
  • Press Ctrl+C in the terminal where Docker is running
  • Or in another terminal: docker stop protege
The --rm flag ensures the container is automatically removed after stopping.

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Troubleshooting

Check:
  • Docker is installed and running
  • You’ve pulled the correct image version
  • Port 8050 is not already in use
Fix port conflicts:
# Use a different port on your host
-p 127.0.0.1:8051:8050
# Then access at http://127.0.0.1:8051
Check:
  • The file exists in your mounted directory
  • You’re using the filename only, not the full path
  • File permissions allow reading
Verify mount:
docker run --rm \
  --mount type=bind,source=/your/path/,target=/root/. \
  ddelgadillo/protege_base:v1.0.2 \
  ls -la /root/
Increase Docker memory allocation:
  • Docker Desktop: Settings → Resources → Memory
  • Recommended: 4GB+ for large datasets
Optimize:
  • Increase --cpus value (up to your system’s core count)
  • Ensure Docker has adequate memory allocated
  • Close other resource-intensive applications

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