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Only delete writable files on job resubmission

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This commit is contained in:
mvdbeek
2020-01-21 11:18:13 +01:00
parent db472b2bc0
commit 8d099ef98b
1 changed files with 4 additions and 6 deletions
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lib/galaxy/jobs/command_factory.py
+4 -6
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@@ -99,15 +99,13 @@ def build_command(
# usually working will already exist, but it will not for task
# split jobs.
# Remove the working directory incase this is for instance a SLURM re-submission.
# Remove all non-readonly files in the workfing directory incase this is a re-submission.
# xref https://github.com/galaxyproject/galaxy/issues/3289
commands_builder.prepend_command("""# Delete working/ and outputs/ only if job was resubmitted
commands_builder.prepend_command("""
if [ -f .job_started ]; then
rm -rf working outputs; mkdir -p working outputs
find working outputs -perm /0222 -delete 2> /dev/null || true
fi
touch .job_started
cd working
""", sep='')
mkdir -p working outputs; touch .job_started; cd working""")
container_monitor_command = job_wrapper.container_monitor_command(container)
if container_monitor_command: