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Today's Topics:

   1. Job Script Integrity (John Letaw)


----------------------------------------------------------------------

Message: 1
Date: Tue, 7 Nov 2017 03:20:49 +0000
From: "John Letaw" <letaw@ohsu.edu>
To: "galaxy-dev@lists.galaxyproject.org"
        <galaxy-dev@lists.galaxyproject.org>
Subject: [galaxy-dev] Job Script Integrity
Message-ID: <FBF795C3-8F01-47EF-8033-F14DD8694328@ohsu.edu>
Content-Type: text/plain; charset="utf-8"

Hi all,

I’m installing via GalaxyKickStart…

I’m getting the following error:

galaxy.jobs.runners ERROR 2017-11-06 19:14:05,263 (19) Failure preparing job
Traceback (most recent call last):
  File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/galaxy/jobs/runners/__init__.py", line 175, in prepare_job
    modify_command_for_container=modify_command_for_container
  File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/galaxy/jobs/runners/__init__.py", line 209, in build_command_line
    container=container
  File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/galaxy/jobs/command_factory.py", line 84, in build_command
    externalized_commands = __externalize_commands(job_wrapper, external_command_shell, commands_builder, remote_command_params)
  File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/galaxy/jobs/command_factory.py", line 143, in __externalize_commands
    write_script(local_container_script, script_contents, config)
  File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/galaxy/jobs/runners/util/job_script/__init__.py", line 112, in write_script
    _handle_script_integrity(path, config)
  File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/galaxy/jobs/runners/util/job_script/__init__.py", line 147, in _handle_script_integrity
    raise Exception("Failed to write job script, could not verify job script integrity.")
Exception: Failed to write job script, could not verify job script integrity.
galaxy.model.metadata DEBUG 2017-11-06 19:14:05,541 Cleaning up external metadata files
galaxy.model.metadata DEBUG 2017-11-06 19:14:05,576 Failed to cleanup MetadataTempFile temp files from /home/exacloud/lustre1/galaxydev/galaxyuser/database/jobs/000/19/metadata_out_HistoryDatasetAssociation_16_I8bhLX: No JSON object could be decoded

I would like to further understand what it means to not verify integrity of a job script.  Does this just mean there is a permissions error?  Ownership doesn’t match up?

Thanks,
John

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