Support for the Docker Socket Solution
Context for this request:
My group wanted to take advantage of a gold standard RNA-seq analysis pipeline developed by Bio-Rad Laboratories for our projects. We were excited to discover that they had developed a docker image of their pipeline, and hoped to implement the docker image in a Terra workflow. Later, I discovered that the pipeline Dockerfile does not specify a CMD for the user and that the ENTRYPOINT they do specify contains an executable script whose contents are unknown. As a result, I was in the dark about how to construct a command in the Terra workflow that would execute properly in the docker environment. However, Bio-Rad did provide a complete (and highly specific) "docker run" command for executing their pipeline in their user guidebook.
Would it be possible to have a runtime option that enables the Docker socket solution (see the section on socket solutions at this link) in Terra? This feature would allow Terra users to run docker images from within a running container set up by the Cromwell compute engine.
Comments
1 comment
Hi Neil Ruthen,
Thanks for the suggestion. I've created a ticket for our product team to consider.
Best,
Samantha
Please sign in to leave a comment.