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cosmic-extract's Introduction

cosmic-extract

Download and extract the cosmic dependencies for g2p

Build

$docker build -t cosmic-extract .

container documentation

$ docker inspect cosmic-extract    | jq -r '.[0].Config.Labels'
{
  "maintainer": "[email protected]",
  "org.label-schema.description": "Download cosmic variants and create tsv(s).",
  "org.label-schema.docker.cmd": "docker run --rm -it -v /tmp:/output -v ~/g2p-aggregator/harvester/CosmicMutantExport.tsv.gz:/g2p-aggregator/harvester/CosmicMutantExport.tsv.gz  cosmic-extract",
  "org.label-schema.name": "g2p cosmic",
  "org.label-schema.usage": "https://github.com/biostream/cosmic-extract/blob/master/README.md",
  "version": "1.0"
}

inputs

outputs

  • /output
  • upload to swift
$ swift upload --object-name cosmic etl-development /tmp/cosmic

Example CWL invocation

cwltool cosmic-extract.cwl test.json

known consumers

cosmic-extract's People

Contributors

bwalsh avatar kellrott avatar

Watchers

Ryan Spangler avatar  avatar  avatar James Cloos avatar

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