4. Running with Dockstore CLI

dockstore-cgpmap can be run with the Dockstore CLI locally for testing purposes.

Requirements

• Docker
• Java 11
• Dockstore CLI
• cwltool

For full installation instructions, see here. Alternatively follow the abbreviated instructions below.

Java 11

sudo add-apt-repository ppa:openjdk-r/ppa && sudo apt-get update -q && sudo apt install -y openjdk-11-jdk

Dockstore CLI

mkdir ~/bin
wget -O ~/bin/dockstore "https://github.com/dockstore/dockstore/releases/download/1.11.8/dockstore"
chmod +x ~/bin/dockstore
export PATH=${PATH}:${HOME}/bin

cwltool

First install Python 3 and pip3, then:

curl -o requirements.txt "https://dockstore.org/api/metadata/runner_dependencies?client_version=1.11.8&python_version=3"
pip3 install -r requirements.txt

Running with Dockstore CLI

Clone the dockstore-cgpmap repository.

To run dockstore-cgpmap with Dockstore, you need a CWL Tool definition file (.cwl) and a json parameter file.

The cwls directory contains multiple CWL Tool definition files.

Copy one of the example .json files in examples/cgpmap, replacing the "reference", "bwa_idx" and "seq_in" with the paths to local files. Other parameters may also be changed.(for a full list of parameters, see here).

The final json file should look like below:

{
  "reference": {
    "path": "file:///home/ubuntu/data/core_ref_GRCh38_hla_decoy_ebv.tar.gz",
    "class": "File"
  },
  "bwa_idx": {
    "path": "file:///home/ubuntu/data/bwa_idx_GRCh38_hla_decoy_ebv_bwamem2.tar.gz",
    "class": "File"
  },
  "seq_in": [
    {
      "path": "file:///home/ubuntu/data/insilico_21.bam",
      "class": "File"
    }
  ],
  "sample": "test",
  "mmqc": false,
  "mmqcfrag": 0.05,
  "threads": 0,
  "bwamem2": true,
  "nomarkdup": false,
  "dupmode": "t",
  "legacy": false,
  "out_bam": {
    "path": "/out.bam",
    "class": "File"
  }
}