bionexus 0.1.0

BioNexus facilitates cross-modal retrieval between natural products and biosynthetic gene clusters

BioNexus

Setting up database

1. Copy .env.example -> .env and adjust

2. Start Postgres + Adminer:

   docker-compose up -d db adminer
   

   Adminer available at http://localhost:8080 (server: db, user: bionexus, db: bionexus)

3. (Optional) Create local env using conda:

   conda create -n bionexus python=3.10
   conda activate bionexus
   pip install -e .[dev]
   

4. Create/upgrade schema:

   bionexus upgrade head
   

5. Load data:

   RetroMol and BioCracker results can be loaded with the load command. For more information, run:

   bionexus load --help
   

   Examples of scripts that extract annotations and references from RetroMol and BioCracker can be found in the scripts/ folder.

6. Dump for deployoment:

   Make sure the database is running in Docker, then:

   bionexus dump --out ~/Downloads/dumps/bionexus_$(date +%Y%m%d).dump