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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
):
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:
compute_tool_directory = job_wrapper.tool.tool_dir
lib/galaxy/tools/deps/containers.py
+1 -1
View File
@@ -298,7 +298,7 @@ class DockerContainer(Container):
defaults = "$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw"
elif self.app_info.outputs_to_working_directory:
# 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"
else:
defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw"