Download and extract the cosmic dependencies for g2p
$docker build -t cosmic-extract .
$ 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"
}
/g2p-aggregator/harvester/CosmicMutantExport.tsv.gz
- you will need to register and download https://grch37-cancer.sanger.ac.uk/cosmic/files?data=/files/grch37/cosmic/v81/CosmicMutantExport.tsv.gz
/output
- upload to swift
$ swift upload --object-name cosmic etl-development /tmp/cosmic
cwltool cosmic-extract.cwl test.json
- g2p-transform https://github.com/biostream/g2p-transform