def docker_galaxy_config(ctx, runnables, for_tests=False, **kwds):
"""Set up a ``GalaxyConfig`` for Docker container."""
tool_paths = [r.path for r in runnables if r.has_tools]
test_data_dir = _find_test_data(tool_paths, **kwds)
with _config_directory(ctx, **kwds) as config_directory:
def config_join(*args):
return os.path.join(config_directory, *args)
ensure_dependency_resolvers_conf_configured(
ctx, kwds, os.path.join(config_directory, "resolvers_conf.xml"))
_handle_job_metrics(config_directory, kwds)
shed_tool_conf = "config/shed_tool_conf.xml"
all_tool_paths = _all_tool_paths(runnables, **kwds)
tool_directories = set([]) # Things to mount...
for tool_path in all_tool_paths:
directory = os.path.dirname(os.path.normpath(tool_path))
if os.path.exists(directory):
tool_directories.add(directory)
# TODO: remap these.
tool_volumes = []
for tool_directory in tool_directories:
volume = simple_docker_volume(tool_directory)
tool_volumes.append(volume)
empty_tool_conf = config_join("empty_tool_conf.xml")
tool_conf = config_join("tool_conf.xml")
shed_tool_path = kwds.get("shed_tool_path") or config_join(
"shed_tools")
_ensure_directory(shed_tool_path)
sheds_config_path = _configure_sheds_config_file(
ctx, config_directory, **kwds)
port = _get_port(kwds)
properties = _shared_galaxy_properties(config_directory,
kwds,
for_tests=for_tests)
_handle_container_resolution(ctx, kwds, properties)
master_api_key = _get_master_api_key(kwds)
template_args = dict(
shed_tool_path=shed_tool_path,
tool_conf=tool_conf,
)
tool_config_file = "%s,%s" % (tool_conf, shed_tool_conf)
_write_tool_conf(ctx, all_tool_paths, tool_conf)
write_file(empty_tool_conf, EMPTY_TOOL_CONF_TEMPLATE)
properties.update(
dict(
tool_config_file=tool_config_file,
tool_sheds_config_file=sheds_config_path,
migrated_tools_config=empty_tool_conf,
))
server_name = "planemo%d" % random.randint(0, 100000)
# Value substitutions in Galaxy properties - for consistency with
# non-Dockerized version.
template_args = dict()
env = _build_env_for_galaxy(properties, template_args)
env["NONUSE"] = "nodejs,proftp,reports"
if ctx.verbose:
env["GALAXY_LOGGING"] = "full"
# TODO: setup FTP upload dir and disable FTP server in container.
_build_test_env(properties, env)
docker_target_kwds = docker_host_args(**kwds)
volumes = tool_volumes + [simple_docker_volume(config_directory)]
export_directory = kwds.get("export_directory", None)
if export_directory is not None:
volumes.append(DockerVolume("%s:/export:rw" % export_directory))
# TODO: Allow this to real Docker volumes and allow multiple.
extra_volume = kwds.get("docker_extra_volume")
if extra_volume:
volumes.append(simple_docker_volume(extra_volume))
yield DockerGalaxyConfig(
ctx,
config_directory,
env,
test_data_dir,
port,
server_name,
master_api_key,
runnables,
docker_target_kwds=docker_target_kwds,
volumes=volumes,
export_directory=export_directory,
kwds=kwds,
)
def docker_galaxy_config(ctx, runnables, for_tests=False, **kwds):
"""Set up a ``GalaxyConfig`` for Docker container."""
tool_paths = [r.path for r in runnables if r.has_tools]
test_data_dir = _find_test_data(tool_paths, **kwds)
with _config_directory(ctx, **kwds) as config_directory:
def config_join(*args):
return os.path.join(config_directory, *args)
ensure_dependency_resolvers_conf_configured(ctx, kwds, os.path.join(config_directory, "resolvers_conf.xml"))
_handle_job_metrics(config_directory, kwds)
shed_tool_conf = "config/shed_tool_conf.xml"
all_tool_paths = _all_tool_paths(runnables, **kwds)
tool_directories = set([]) # Things to mount...
for tool_path in all_tool_paths:
directory = os.path.dirname(os.path.normpath(tool_path))
if os.path.exists(directory):
tool_directories.add(directory)
# TODO: remap these.
tool_volumes = []
for tool_directory in tool_directories:
volume = simple_docker_volume(tool_directory)
tool_volumes.append(volume)
empty_tool_conf = config_join("empty_tool_conf.xml")
tool_conf = config_join("tool_conf.xml")
shed_tool_path = kwds.get("shed_tool_path") or config_join("shed_tools")
_ensure_directory(shed_tool_path)
sheds_config_path = _configure_sheds_config_file(
ctx, config_directory, **kwds
)
port = _get_port(kwds)
properties = _shared_galaxy_properties(config_directory, kwds, for_tests=for_tests)
_handle_container_resolution(ctx, kwds, properties)
master_api_key = _get_master_api_key(kwds)
template_args = dict(
shed_tool_path=shed_tool_path,
tool_conf=tool_conf,
)
tool_config_file = "%s,%s" % (tool_conf, shed_tool_conf)
_write_tool_conf(ctx, all_tool_paths, tool_conf)
write_file(empty_tool_conf, EMPTY_TOOL_CONF_TEMPLATE)
properties.update(dict(
tool_config_file=tool_config_file,
tool_sheds_config_file=sheds_config_path,
migrated_tools_config=empty_tool_conf,
))
server_name = "planemo%d" % random.randint(0, 100000)
# Value substitutions in Galaxy properties - for consistency with
# non-Dockerized version.
template_args = dict(
)
env = _build_env_for_galaxy(properties, template_args)
env["NONUSE"] = "nodejs,proftp,reports"
if ctx.verbose:
env["GALAXY_LOGGING"] = "full"
# TODO: setup FTP upload dir and disable FTP server in container.
_build_test_env(properties, env)
docker_target_kwds = docker_host_args(**kwds)
volumes = tool_volumes + [simple_docker_volume(config_directory)]
export_directory = kwds.get("export_directory", None)
if export_directory is not None:
volumes.append(DockerVolume("%s:/export:rw" % export_directory))
# TODO: Allow this to real Docker volumes and allow multiple.
extra_volume = kwds.get("docker_extra_volume")
if extra_volume:
volumes.append(simple_docker_volume(extra_volume))
yield DockerGalaxyConfig(
ctx,
config_directory,
env,
test_data_dir,
port,
server_name,
master_api_key,
runnables,
docker_target_kwds=docker_target_kwds,
volumes=volumes,
export_directory=export_directory,
kwds=kwds,
)