Deployment

Local Development

git clone https://github.com/lcerdeira/plasmidnet.git
cd plasmidnet
pip install -r requirements.txt
python build_db.py    # ~2 min, downloads 200 MB from Figshare
python app.py         # http://localhost:8050

Requirements

Python 3.9+
BLAST+ (for plasmid comparison): brew install blast or apt install ncbi-blast+
~500 MB disk space for the database

Heroku

PlasmidNet is deployed on Heroku with automatic database building.

heroku create plasmidnet
git push heroku main
heroku open

How it works

heroku-community/apt buildpack installs ncbi-blast+ from Aptfile
heroku/python buildpack installs pip packages from requirements.txt
bin/post_compile hook:
- Downloads PLSDB CSVs from Figshare
- Filters proteins.csv for TA/phage/transposase genes
- Harvests additional plasmids from NCBI
- Builds the SQLite database
- Pre-builds the correlations cache

Heroku Limits

RAM: 512 MB (Eco dyno). App uses ~107 MB at startup.
Slug size: 500 MB limit. Current: ~140 MB.
Ephemeral filesystem: Database is rebuilt on each deploy.

Buildpacks

1. heroku-community/apt      (installs BLAST+)
2. heroku/python              (installs pip packages)

Render (free tier)

Connect your GitHub repo at render.com
Create a new Web Service
Set build command: pip install -r requirements.txt && bash bin/post_compile
Set start command: gunicorn app:server --bind 0.0.0.0:$PORT

Docker (optional)

FROM python:3.12-slim
RUN apt-get update && apt-get install -y ncbi-blast+ curl && rm -rf /var/lib/apt/lists/*
WORKDIR /app
COPY requirements.txt .
RUN pip install -r requirements.txt
COPY . .
RUN bash bin/post_compile
CMD gunicorn app:server --bind 0.0.0.0:$PORT

EC2 Pipeline (MOBsuite + AMRFinderPlus)

For typing the 109K NCBI plasmids:

# On EC2 (c6i.4xlarge or larger, 50 GB disk)
scp ec2_run.sh ec2-user@<ip>:/data/plasmidnet_pipeline/
scp data/ncbi_accessions.txt ec2-user@<ip>:/data/plasmidnet_pipeline/
ssh ec2-user@<ip>
cd /data/plasmidnet_pipeline
nohup bash run_now.sh > pipeline.log 2>&1 &

# Monitor
tail -f pipeline.log

# When done, download results
scp ec2-user@<ip>:/data/plasmidnet_pipeline/results/mob_results.csv .
scp ec2-user@<ip>:/data/plasmidnet_pipeline/results/amr_results.tsv .

# Import
python import_mobsuite_results.py mob_results.csv amr_results.tsv