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dxCompiler Docker Image

Steps to build and run a Docker image with dxCompiler, as an alternative to installing Java and running the dxCompiler.jar locally.

Build Docker

  1. Specify the dxCompiler version to use here.
  2. Run docker_build

Run Docker

  1. Login to DNAnexus with dx login and select a project.
  2. Run docker_run with dxCompiler args as args.
./docker_run.sh -help
  • For compiling a workflow, the local working directory is mounted to the container.
# General example
<path to docker_run.sh> compile <path to WDL source>

# From dxCompiler repo directory
./scripts/docker_image/docker_run.sh compile test/single_tasks/add3.wdl