Hi John,
Can you also raise an issue in https://github.com/ARTbio/ GalaxyKickStart/issues ?
In order to help, I will need to know the configuration of your GalaxyKickStart (the variables you modified in the playbook, group_vars and inventory_files).
Did you use the cloud_setup role ? In that case Enis Afgan https://github.com/afgane may help.
Best regards
Chris
Christophe Antoniewski
Institut de Biologie Paris Seine http://www.ibps.upmc.fr/en 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 ARTbio http://artbio.fr/ Bâtiment B, 7e étage, porte 725
Tel +33 1 44 2 *7 70 05*Mobile +33 6 68 60 51 50 <06%2068%2060%2051%2050>
Pour accéder à la Plateforme Bâtiment B, 7e étage, Porte 725 https://www.google.com/maps/d/u/0/edit?mid=zmZz-3Vin5D0.kjRSV6vitXE8
https://twitter.com/ARTbio_IBPS
2017-11-07 18:00 GMT+01:00 galaxy-dev-request@lists.galaxyproject.org:
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Today's Topics:
- 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/galaxyd ev/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