Unverified Commit e667761d authored by Nate Coraor's avatar Nate Coraor
Browse files

Allow specifying a command for determining a docker host port

parent 3b215326

lib/galaxy/config/sample/job_conf.sample.yml

+5 −0
Original line number Diff line number Diff line
@@ -503,6 +503,11 @@ execution: 
      # Following command can be used to tweak docker command.

      #docker_cmd: /usr/local/custom_docker/docker



      # Docker containers that expose ports (e.g. Interactive Tools) can

      # optionally use a command to determine the host port that is exposed. By

      # default, one is chosen at random (docker run -p <guest_port> ...).

      #docker_host_port_cmd:



      # Following can be used to connect to docker server in different

      # ways (translated as -H argument to docker client).

      #docker_host: unix:///var/run/docker.sock

lib/galaxy/tool_util/deps/container_classes.py

+1 −0
Original line number Diff line number Diff line
@@ -481,6 +481,7 @@ class DockerContainer(Container, HasDockerLikeVolumes): 
            set_user=self.prop("set_user", docker_util.DEFAULT_SET_USER),

            run_extra_arguments=self.prop("run_extra_arguments", docker_util.DEFAULT_RUN_EXTRA_ARGUMENTS),

            guest_ports=self.tool_info.guest_ports,

            host_port_cmd=self.prop("host_port_cmd", None),

            container_name=self.container_name,

            **docker_host_props,

        )

lib/galaxy/tool_util/deps/docker_util.py

+6 −1
Original line number Diff line number Diff line
@@ -111,6 +111,7 @@ def build_docker_run_command( 
    set_user: Optional[str] = DEFAULT_SET_USER,

    host: Optional[str] = DEFAULT_HOST,

    guest_ports: Union[bool, str, List[str]] = False,

    host_port_cmd: Optional[str] = None,

    container_name: Optional[str] = None,

) -> str:

    env_directives = env_directives or []
@@ -129,10 +130,14 @@ def build_docker_run_command( 
        # When is True, expose all ports

        command_parts.append("-P")

    elif guest_ports:

        if host_port_cmd:

            host_port_cmd = f"$({host_port_cmd}):"

        else:

            host_port_cmd = ""

        if not isinstance(guest_ports, list):

            guest_ports = [guest_ports]

        for guest_port in guest_ports:

            command_parts.extend(["-p", guest_port])

            command_parts.extend(["-p", f"{host_port_cmd}{guest_port}"])

    if container_name:

        command_parts.extend(["--name", container_name])

    for volume in volumes: