biostream/cosmic-extract

Name: cosmic-extract

Owner: biostream

Description: create the dependencies used by g2p-transform

Created: 2017-10-03 20:15:09.0

Updated: 2017-10-25 16:34:25.0

Pushed: 2017-10-25 16:34:23.0

Homepage: null

Size: 4

Language: Shell

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README

cosmic-extract

Download and extract the cosmic dependencies for g2p

Build

ker build -t cosmic-extract .

container documentation

cker inspect cosmic-extract    | jq -r '.[0].Config.Labels'

aintainer": "walsbr@ohsu.edu",
rg.label-schema.description": "Download cosmic variants and create tsv(s).",
rg.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",
rg.label-schema.name": "g2p cosmic",
rg.label-schema.usage": "https://github.com/biostream/cosmic-extract/blob/master/README.md",
ersion": "1.0"

inputs

• /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

outputs

• /output
• upload to swift

ift upload --object-name cosmic etl-development /tmp/cosmic

Example CWL invocation

ool cosmic-extract.cwl test.json

known consumers

• g2p-transform https://github.com/biostream/g2p-transform