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 <[email protected]>: > Send galaxy-dev mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.galaxyproject.org/listinfo/galaxy-dev > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-dev digest..." > > > HEY! This is important! If you reply to a thread in a digest, please > 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to > the original subject for the thread. > 2. Strip out everything else in the digest that is not part of the thread > you are responding to. > > Why? > 1. This will keep the subject meaningful. People will have some idea from > the subject line if they should read it or not. > 2. Not doing this greatly increases the number of emails that match search > queries, but that aren't actually informative. > > Today's Topics: > > 1. Job Script Integrity (John Letaw) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 7 Nov 2017 03:20:49 +0000 > From: "John Letaw" <[email protected]> > To: "[email protected]" > <[email protected]> > Subject: [galaxy-dev] Job Script Integrity > Message-ID: <[email protected]> > 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 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attach > ments/20171107/66103ce8/attachment-0001.html> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > galaxy-dev mailing list > [email protected] > https://lists.galaxyproject.org/listinfo/galaxy-dev > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > ------------------------------ > > End of galaxy-dev Digest, Vol 137, Issue 5 > ****************************************** >
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