Skip to content

Docker.md

Latest commit

 

History

History
81 lines (62 loc) · 2.1 KB

Docker.md

File metadata and controls

81 lines (62 loc) · 2.1 KB

Docker Usage

This repo includes a two-stage Dockerfile that builds the spades conda environment, installs the vendored GOTTCHA2 package, and copies the runtime files into a slim Debian image.

Local Build

From the repo root:

docker build -t spades-g2:local .

Optional multi-platform publish examples:

docker buildx build --platform linux/arm64 -t spades-g2:[DATE]-arm64 .
docker buildx build --platform linux/amd64 -t spades-g2:[DATE]-amd64 .
docker buildx build --platform linux/amd64,linux/arm64 -t spades-g2:[DATE] -t spades-g2:latest .

Check The Image

The image contains data/, scripts/, run_SPADES.sh, and post_install.sh. Run the lightweight install checker before using a new image:

docker run --rm -it spades-g2:local ./scripts/check_install.sh

The checker does not run the sequencing workflow. It verifies required command line tools, Python imports, SPADES data files, and Krona taxonomy wiring.

Run

Mount your reads and database into the container so the pipeline can read inputs and write outputs back to the host filesystem.

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

Notes:

  • -d expects the GOTTCHA2 fast-profile database base path without extensions.
  • The database directory must contain:
    • <db>.syldb
    • <db>.zip
    • <db>.stats
    • <db>.tax.tsv
  • The image already contains data/taxonomy_db and data/pathogen.tsv.
  • Add --ont to run_SPADES.sh for long-read single-end inputs.
  • Use --js-external unless the HTML reports will be served from an environment that provides the local /publicdata JavaScript/CSS assets.

Run The Bundled Test

The runtime image does not bake in the full test/ directory. Mount the repo if you want to run the bundled test script:

docker run --rm -it \
  -v "$PWD":/work \
  -w /work/test \
  spades-g2:local \
  ./test_run.sh