Skip to content

Latest commit

 

History

History
22 lines (17 loc) · 1.4 KB

README.md

File metadata and controls

22 lines (17 loc) · 1.4 KB
Raw

Quick start

Find an image at github.com/orgs/ucladx/packages and run it using docker or singularity like this:

docker run --rm ghcr.io/ucladx/<image>:<version> <command>
singularity exec docker://ghcr.io/ucladx/<image>:<version> <command>

For example, to display bwa mem command-line usage using the ucladx/bwa:0.7.17 image:

docker run --rm ghcr.io/ucladx/bwa:0.7.17 bwa mem
singularity exec docker://ghcr.io/ucladx/bwa:0.7.17 bwa mem

If mounting writable volumes with docker on Linux, use -u to control ownership of output files (default is root:root):

docker run --rm -v $PWD:/mnt -w /mnt -u $(id -u):$(id -g) ghcr.io/ucladx/gatk:4.1.9.0 gatk FuncotatorDataSourceDownloader --somatic --output FuncotatorSomatic

Install docker or singularity

Follow these instructions to install docker. It requires administrative rights, which you normally have on a laptop/workstation. But if not, contact your system administrator to get Docker installed. In shared computers like HPC clusters, they might have valid concerns against installing Docker. If so, ask them to follow these instructions to install singularity instead. If they still say no, then ask your boss to convince them.