Exemplo n.º 1
0
def cli(ctx, path, **kwds):
    """Launch a shell in the Docker container referenced by the specified
    tool. Prints a command to do this the way Galaxy would in job files it
    generates - so be sure to wrap this in $(...) to launch the subshell.::

        % $(planemo docker_shell bowtie2.xml)
        ...
        root@b8754062f875:/#

    """
    tool_xml = load_tool(path)
    requirements, containers = parse_requirements_from_xml(tool_xml)
    identifier = None
    for container in containers:
        if container.type == "docker":
            identifier = container.identifier

    if kwds["from_tag"]:
        identifier = "-t %s" % identifier

    script = docker_util.build_docker_run_command(
        "/bin/bash",
        identifier,
        interactive=True,
        **dockerfiles.docker_host_args(**kwds)
    )
    print(script)
Exemplo n.º 2
0
def cli(ctx, path, **kwds):
    """Launch a shell in the Docker container referenced by the specified
    tool. Prints a command to do this the way Galaxy would in job files it
    generates - so be sure to wrap this in $(...) to launch the subshell.::

        % $(planemo docker_shell bowtie2.xml)
        ...
        root@b8754062f875:/#

    """
    tool_xml = load_tool(path)
    requirements, containers = parse_requirements_from_xml(tool_xml)
    identifier = None
    for container in containers:
        if container.type == "docker":
            identifier = container.identifier

    if kwds["from_tag"]:
        identifier = "-t %s" % identifier

    script = docker_util.build_docker_run_command(
        "/bin/bash",
        identifier,
        interactive=True,
        **dockerfiles.docker_host_args(**kwds))
    print(script)
 def __init__(self, **kwds):
     """Construct a postgres database source from planemo configuration."""
     self.psql_path = 'psql'
     self.database_user = '******'
     self.database_password = DEFAULT_POSTGRES_PASSWORD
     self.database_host = 'localhost'  # TODO: Make docker host
     self.database_port = DEFAULT_POSTGRES_PORT_EXPOSE
     self._kwds = kwds
     self._docker_host_kwds = dockerfiles.docker_host_args(**kwds)
     if not is_running_container(**self._docker_host_kwds):
         start_postgres_docker(**self._docker_host_kwds)
         # Hack to give docker a bit of time to boot up and allow psql to start.
         time.sleep(30)
Exemplo n.º 4
0
def cli(ctx, path, **kwds):
    """Launch shell in Docker container for a tool.

    Will launch a shell in the Docker container referenced by the specified
    tool. Prints a command to do this the way Galaxy would in job files it
    generates - so be sure to wrap this in $(...) to launch the subshell.

    \b
        $ $(planemo docker_shell bowtie2.xml)
        ...
        root@b8754062f875:/#

    """
    tool_xml = load_tool(path)
    requirements, containers = parse_requirements_from_xml(tool_xml)
    identifier = None
    for container in containers:
        if container.type == "docker":
            identifier = container.identifier

    # Refactor mulled container resolver to be able to do this.
    if kwds["from_tag"]:
        identifier = "-t %s" % identifier

    tool_dir = os.path.dirname(os.path.abspath(path))
    working_dir = os.path.abspath(os.getcwd())
    if tool_dir.startswith(working_dir):
        volumes = [
            "%s:%s" % (working_dir, working_dir)
        ]
    elif working_dir.startswith(tool_dir):
        volumes = [
            "%s:%s" % (tool_dir, tool_dir)
        ]
    else:
        volumes = [
            "%s:%s" % (working_dir, working_dir),
            "%s:%s" % (tool_dir, tool_dir)
        ]

    script = docker_util.build_docker_run_command(
        "/bin/bash",
        identifier,
        interactive=True,
        terminal=True,
        working_directory=working_dir,
        volumes=volumes,
        **dockerfiles.docker_host_args(**kwds)
    )
    print(script)
Exemplo n.º 5
0
def cli(ctx, path, **kwds):
    """Launch shell in Docker container for a tool.

    Will launch a shell in the Docker container referenced by the specified
    tool. Prints a command to do this the way Galaxy would in job files it
    generates - so be sure to wrap this in $(...) to launch the subshell.::

        % $(planemo docker_shell bowtie2.xml)
        ...
        root@b8754062f875:/#

    """
    tool_xml = load_tool(path)
    requirements, containers = parse_requirements_from_xml(tool_xml)
    identifier = None
    for container in containers:
        if container.type == "docker":
            identifier = container.identifier

    if kwds["from_tag"]:
        identifier = "-t %s" % identifier

    tool_dir = os.path.dirname(os.path.abspath(path))
    working_dir = os.path.abspath(os.getcwd())
    if tool_dir.startswith(working_dir):
        volumes = [
            "%s:%s" % (working_dir, working_dir)
        ]
    elif working_dir.startswith(tool_dir):
        volumes = [
            "%s:%s" % (tool_dir, tool_dir)
        ]
    else:
        volumes = [
            "%s:%s" % (working_dir, working_dir),
            "%s:%s" % (tool_dir, tool_dir)
        ]

    script = docker_util.build_docker_run_command(
        "/bin/bash",
        identifier,
        interactive=True,
        terminal=True,
        working_directory=working_dir,
        volumes=volumes,
        **dockerfiles.docker_host_args(**kwds)
    )
    print(script)