Job Script Integrity

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Job Script Integrity

John Letaw

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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