Skip to content

Instantly share code, notes, and snippets.

@agaszmurlo

agaszmurlo/docker_test.sh

Created May 10, 2019 13:59
Show Gist options
  • Save agaszmurlo/3fa7a380c2b9db927eb73f707be9e47b to your computer and use it in GitHub Desktop.
Save agaszmurlo/3fa7a380c2b9db927eb73f707be9e47b to your computer and use it in GitHub Desktop.
Download ZIP
Raw
docker_test.sh
docker pull biodatageeks/bdg-sequila:0.5.5-spark-2.4.2-SNAPSHOT
docker run -it --rm \
-e USERID=$UID -e GROUPID=$(id -g) \
-v /Users/aga/workplace/data/slice:/data \
biodatageeks/bdg-sequila:0.5.5-spark-2.4.2-SNAPSHOT \
depthOfCoverage \
--master=local --driver-memory=8g \
-- \
--reads /data/NA12878.slice.bam --format blocks -o /data/NA12878.cov.bed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment