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Merge pull request #1974 from jmchilton/docker_fix

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Fix docker tool execution for #1688.
This commit is contained in:
Dannon Baker
2016-03-22 12:42:16 -04:00
parent 67b7294a72 975937ec9d
commit 0dc57b08e8
3 changed files with 5 additions and 3 deletions
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lib/galaxy/jobs/runners/__init__.py
+1 -1
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@@ -322,7 +322,7 @@ class BaseJobRunner( object ):
compute_job_directory=None compute_job_directory=None
): ):
if not compute_working_directory: if not compute_working_directory:
compute_working_directory = job_wrapper.working_directory compute_working_directory = job_wrapper.tool_working_directory
if not compute_tool_directory: if not compute_tool_directory:
compute_tool_directory = job_wrapper.tool.tool_dir compute_tool_directory = job_wrapper.tool.tool_dir
lib/galaxy/tools/deps/containers.py
+1 -1
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@@ -298,7 +298,7 @@ class DockerContainer(Container):
defaults = "$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw" defaults = "$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw"
elif self.app_info.outputs_to_working_directory: elif self.app_info.outputs_to_working_directory:
# Should need default_file_path (which is a course estimate given # Should need default_file_path (which is a course estimate given
# object stores anyway. # object stores anyway).
defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:ro" defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:ro"
else: else:
defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw" defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw"
test/unit/jobs/test_runner_local.py
+3 -1
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@@ -101,7 +101,8 @@ class MockJobWrapper( object ):
def __init__( self, app, test_directory, tool ): def __init__( self, app, test_directory, tool ):
working_directory = os.path.join( test_directory, "workdir" ) working_directory = os.path.join( test_directory, "workdir" )
os.makedirs( working_directory ) tool_working_directory = os.path.join( working_directory, "working" )
os.makedirs( tool_working_directory )
self.app = app self.app = app
self.tool = tool self.tool = tool
self.state = model.Job.states.QUEUED self.state = model.Job.states.QUEUED
@@ -112,6 +113,7 @@ class MockJobWrapper( object ):
self.write_version_cmd = None self.write_version_cmd = None
self.dependency_shell_commands = None self.dependency_shell_commands = None
self.working_directory = working_directory self.working_directory = working_directory
self.tool_working_directory = tool_working_directory
self.requires_setting_metadata = True self.requires_setting_metadata = True
self.job_destination = bunch.Bunch( id="default", params={} ) self.job_destination = bunch.Bunch( id="default", params={} )
self.galaxy_lib_dir = os.path.abspath( "lib" ) self.galaxy_lib_dir = os.path.abspath( "lib" )