bioboxes/soap repository overview

⁠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)