poeli/spades-g2 repository overview

⁠Docker usage

This repo includes a two-stage Dockerfile that builds a conda env with the pipeline dependencies and copies it into a slim runtime image.

⁠Run

Mount your local data and database into the container so the pipeline can read them and write outputs back to your host filesystem.

docker run --rm -it \
  -v "$PWD":/app \
  -v /path/to/gottcha_db:/db:ro \
  -w /app \
  poeli/spades-g2:latest \
  ./run_SPADES.sh \
    -i /app/reads.fastq.gz \
    -o /app/outdir \
    -p sample \
    -d /db/gottcha_db.species.fna \
    --js-external \
    -t 8 \
    --spades-data /app/data

Notes:

• -d expects the base path without extensions. The files /db/gottcha_db.species.fna.mmi, /db/gottcha_db.species.fna.stats, and /db/gottcha_db.species.fna.tax.tsv must exist.
• The image already contains data/taxonomy_db and data/pathogen.tsv.
• Add --ont to run_SPADES.sh for long-read inputs.

⁠Run the bundled test (optional)

The repo includes a small test dataset and test script.

docker run --rm -it \
  -v "$PWD":/app \
  -w /app \
  poeli/spades-g2:latest \
  ./test_run.sh