dockstore-tool-md5sum

This is an extremely simple tool, simply used to show how to call a tool via Dockstore. A repo for the Dockerfile to create a Docker image for the md5sum command. Also contains the Dockstore.cwl which is used by the Dockstore to register this container and describe how to call md5sum for the community.

Validation

This tool has been validated as a CWL v1.0 launched using Dockstore 1.1.2.

Versions of dependencies that we tested include:

setuptools==28.8.0
cwltool==1.0.20161114152756
schema-salad==1.18.20161005190847
avro==1.8.1

Building Locally

Normally you would let Quay.io build this. But, if you need to build manually, locally you would execute:

docker build -t quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4 .

WDL Testing

How to execute this tool with Cromwell using the WDL descriptor.

Testing Locally with Cromwell

This tool can be found at the Cromwell project GitHub page.

Make a Parameters JSON

This is the parameterization of the md5sum tool, a copy is present in this repo called test.wdl.json:

{
 "ga4ghMd5.inputFile": "md5sum.input"
}

Run with the CLI

Run it using the cromwell command:

# run this with cromwell (or java -jar cromwell.jar depending on how you installed cromwell)
$> cromwell run Dockstore.wdl test.wdl.json

It will tell you the location of the output file which, in the CWL example below, is specified in the param json file.

CWL Testing

How to execute this tool using the CWL descriptor via the Dockstore command line (which calls the cwltool command behind the scenes).

Testing Locally with the Dockstore CLI

This tool can be found at the Dockstore, login with your GitHub account and follow the directions to setup the CLI. It lets you run a Docker container with a CWL descriptor locally, using Docker and the CWL command line utility. This is great for testing.

Make a Parameters JSON

This is the parameterization of the md5sum tool, a copy is present in this repo called test.dockstore.json:

{
  "input_file": {
        "class": "File",
        "path": "md5sum.input"
    },
    "output_file": {
        "class": "File",
        "path": "/tmp/md5sum.txt"
    }
}

You will also see a test.json file which is the same but with the "output_file" removed. This means when you run it via the Dockstore CLI you need to find the output by looking at the cwltool STDOUT e.g. look at this file:

Saving copy of cwltool stdout to: /Users/boconnor/Development/gitroot/dockstore-tool-md5sum/./datastore/launcher-002bcb21-11e2-47d4-96f5-fb542eb48bb5/outputs/cwltool.stdout.txt

This will tell you the location of the output md5sum file.

You might need to use this "output_file" free test.json if you are executing a more strict CWL execution engine like Arvados.

Run with the CLI

Run it using the dockstore CLI locally with the Dockstore.cwl file (great for testing if you make changes locally):

# run this locally
$> dockstore tool launch --entry Dockstore.cwl --local-entry --json test.json

Or you can run it from the latest release on Dockstore:

# run this from the Dockstore
$> dockstore tool launch --entry quay.io/briandoconnor/dockstore-tool-bamstats:1.0.4 --json test.json

Test with travis-ci

See the .travis.yml file.

Publishing

At this point you follow the SOP from the Dockstore.org site.