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jmchiltonjmchilton
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Implement docker_galaxy engine type.
Specifying ``--engine docker_galaxy`` causes serve, test, and run operations to be backed with a Dockerized Galaxy instance powered by @bgruening's docker-galaxy-stable (https://github.com/bgruening/docker-galaxy-stable). Requires various docker_util and command quoting improvements in galaxy-lib in 16.7.7 (galaxyproject/galaxy-lib@38eca73). Fixes #15.
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-55
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‎planemo/docker.py‎

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"""Docker utilities for planemo.
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Built on Galaxy abstractions in :module:`galaxy.tools.deps.dockerfiles` and
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:module:`galaxy.tools.deps.docker_util`.
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"""
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from __future__ import absolute_import
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from galaxy.tools.deps.dockerfiles import docker_host_args
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__all__ = [
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'docker_host_args',
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]

‎planemo/engine/factory.py‎

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import contextlib
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from .galaxy import GalaxyEngine
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from .galaxy import DockerizedGalaxyEngine
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from .cwltool import CwlToolEngine
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UNKNOWN_ENGINE_TYPE_MESSAGE = "Unknown engine type specified [%s]."
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def build_engine(ctx, **kwds):
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"""Build an engine from the supplied planemo configuration."""
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engine_type_str = kwds.get("engine", "galaxy")
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if engine_type_str == "galaxy":
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engine_type = GalaxyEngine
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elif engine_type == "dockerize_galaxy":
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engine_type = DockerizedGalaxyEngine
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elif engine_type_str == "cwltool":
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engine_type = CwlToolEngine
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else:

‎planemo/engine/galaxy.py‎

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@@ -31,8 +31,23 @@ def _run(self, runnable, job_path):
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@contextlib.contextmanager
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def _serve(self, runnables):
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with serve_daemon(self._ctx, runnables, **self._kwds) as config:
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with serve_daemon(self._ctx, runnables, **self._serve_kwds()) as config:
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yield config
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def _serve_kwds(self):
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return self._kwds.copy()
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__all__ = ["GalaxyEngine"]
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class DockerizedGalaxyEngine(GalaxyEngine):
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"""An :class:`Engine` implementation backed by Galaxy running in Docker.
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More information on Galaxy can be found at http://galaxyproject.org/.
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"""
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def _serve_kwds(self):
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serve_kwds = self._kwds.copy()
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serve_kwds["dockerize"] = True
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return serve_kwds
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__all__ = ["GalaxyEngine", "DockerizedGalaxyEngine"]

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