Merge Planemo and Galaxy tools.deps changes (and a PEP-8 fix)

lib/galaxy/tools/deps/commands.py

@@ -3,15 +3,21 @@
 
 
 def shell(cmds, env=None):
+    p = shell_process(cmds, env)
+    return p.wait()
+
+
+def shell_process(cmds, env=None, **kwds):
     popen_kwds = dict(
         shell=True,
     )
+    popen_kwds.update(**kwds)
     if env:
         new_env = os.environ.copy()
         new_env.update(env)
         popen_kwds["env"] = new_env
     p = subprocess.Popen(cmds, **popen_kwds)
-    return p.wait()
+    return p
 
 
 def execute(cmds):

lib/galaxy/tools/deps/docker_util.py

@@ -76,6 +76,15 @@ def build_save_image_command(
     return build_command_parts
 
 
+def build_pull_command(
+    tag,
+    **kwds
+):
+    build_command_parts = __docker_prefix(**kwds)
+    build_command_parts.extend(["pull", tag])
+    return build_command_parts
+
+
 def build_docker_cache_command(
     image,
     **kwds
@@ -109,6 +118,7 @@ def build_docker_run_command(
     container_command,
     image,
     interactive=False,
+    terminal=False,
     tag=None,
     volumes=[],
     volumes_from=DEFAULT_VOLUMES_FROM,
@@ -134,6 +144,8 @@ def build_docker_run_command(
     command_parts.append("run")
     if interactive:
         command_parts.append("-i")
+    if terminal:
+        command_parts.append("-t")
     for env_directive in env_directives:
         command_parts.extend(["-e", env_directive])
     for volume in volumes:

lib/galaxy/tools/deps/dockerfiles.py

@@ -39,11 +39,16 @@ def dockerfile_build(path, dockerfile=None, error=log.error, **kwds):
     image_identifier = expected_container_names.pop()
 
     dockerfile = __find_dockerfile(dockerfile, tool_directories)
-    docker_command_parts = docker_util.build_command(
-        image_identifier,
-        dockerfile,
-        **docker_host_args(**kwds)
-    )
+    if dockerfile is not None:
+        docker_command_parts = docker_util.build_command(
+            image_identifier,
+            dockerfile,
+            **docker_host_args(**kwds)
+        )
+    else:
+        docker_command_parts = docker_util.build_pull_command(image_identifier, **docker_host_args(**kwds))
+        commands.execute(docker_command_parts)
+
     commands.execute(docker_command_parts)
     docker_image_cache = kwds['docker_image_cache']
     if docker_image_cache:
@@ -67,4 +72,4 @@ def __find_dockerfile(dockerfile, tool_directories):
         potential_dockerfile = os.path.join(directory, "Dockerfile")
         if os.path.exists(potential_dockerfile):
             return potential_dockerfile
-    raise Exception("Could not find dockerfile to build.")
+    return None

lib/galaxy/tools/deps/resolvers/modules.py

@@ -8,7 +8,7 @@
 """
 from os import environ, pathsep
 from os.path import exists, isdir, join
-from StringIO import StringIO
+from six import StringIO
 from subprocess import Popen, PIPE
 
 from ..resolvers import DependencyResolver, INDETERMINATE_DEPENDENCY, Dependency
@@ -112,7 +112,7 @@ def has_module(self, module, version):
         return False
 
     def __modules(self):
-        raw_output = self.__module_avail_output()
+        raw_output = self.__module_avail_output().decode("utf-8")
         for line in StringIO(raw_output):
             line = line and line.strip()
             if not line or line.startswith("-"):