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Soap Assembler

Signature: soap:[fastq A],[fragment_size B] -> contigs C, scaffolds D

Quickstart

  1. git clone https://github.com/bioboxes/soap
  2. cd soap
  3. docker build -t soap .
  4. sudo docker run -v /path/to/your/assembler.yaml:/bbx/input/biobox.yaml -v /path/to/reads.fastq.gz:/bbx/input/test1/reads.fastq.gz -v /path/to/output:/bbx/output ray default

Example biobox.yaml:

---
version: 0.9.0
arguments:
    - fastq:
      - id: "pe" 
        value: "/bbx/input/test1/reads.fastq.gz"
        type: single
    - fragment_size:
      - id: "pe"
        value: 123

Required

  • biobox.yaml : Please see https://github.com/bioboxes/rfc/issues/90 for current definition.
  • gzipped reads with the path provided in biobox.yaml
  • mount your input files to /bbx/input.
  • mount your output directory to /bbx/output
  • mount your biobox.yaml to /bbx/input/biobox.yaml
  • "default" task at the end of your docker run command

####!Note this is not meant for production, it is a showcase for

  • checking a provided yaml against a json-schema schema
  • provide different parameters for an assembler (paired,single,fragment_size)
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