May 2018 - galaxy-dev - lists.galaxyproject.org

by evan clark

I remember there previously being an additional tool that ran on a different port from galaxy that allowed for monitoring of performance and jobs running. Is this tool still packaged with galaxy and if so how can it be activated.

2 years

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Job Script Integrity

by 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

2 years, 3 months

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argparse -> tool xml advice

by Matthias Bernt

Dear list, just a question for advice: I plan to wrap a python script (with lots of options) which uses the argparse library. I was wondering if somebody has an idea to generate the tool xml (semi-)automatically? For instance, by subclassing the formatter, parsing the python code, or parsing the command line... Cheers, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

2 years, 4 months

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Conda problem

by David Lee

Hi, I hope somebody can help me with this. I've been maintaining a Galaxy installation for the past few months that has suddenly developed a problem that I can't undo. I think it occurred after installing samtools and sambamba packages which I have subsequently uninstalled but which has made no difference. Every tool I try to run fails with this error: "Conda dependency failed to build job environment. This is most likely a limitation in conda. You can try to shorten the path to the job_working_directory." Also, in the paster.log file I'm seeing this error that I've never seen before: "CondaError: RuntimeError('EnforceUnusedAdapter called with url https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2018.4.16... command is using a remote connection in offline mode.\n',)" Any suggestions? Regards, David

2 years, 4 months

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The Galaxy release 18.05 is out

by Martin Čech

Dear Community, We are happy to release Galaxy 18.05. Many thanks to committers and you, the community. Enjoy the on time release and please let us know if you face any issues. The release notes are available at https://docs.galaxyproject.org/en/release_18.05/releases/18.05_announce.html Thanks for using Galaxy! Martin, on behalf of the Galaxy committers

2 years, 4 months

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Workflow renaming problem for tool with multiple outputs (Galaxy version 17.09)

by Previti

Hi everybody, I'd like to fix this bug in our local galaxy instance...it's with regard to the erroneous renaming of output files, when there are multiple outputs available. The relevant ticket is the following: https://github.com/galaxyproject/galaxy/pull/5021 Unfortunately a quick update to the newest Galaxy version is not possible for us at the moment. Any tips on how I could do this? Thanks and best regards, Christopher Previti -- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661 christopher.previti(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist. Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung. Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.

2 years, 4 months

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Purging "Monitor installing repositories"

by Previti

Dear all, I've been having an issue with the "Monitor installing repositories" page. There is a whole list of tools that were not installed properly (usually they got interrupted for some reason) and they aren't being removed. Is there a way to purge this list manually? Thanks and best regards, Christopher Previti <http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/monitor_reposito...> -- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661 christopher.previti(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist. Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung. Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.

2 years, 4 months

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Text file busy and conda

by John Letaw

Hi all, I’m receiving the following error trying to access tools autoinstalled via conda: Fatal error: Exit code 126 () ~/galaxy/database/jobs_directory/000/38/tool_script.sh: line 41: ~/galaxy/database/dependencies/_conda/envs/mulled-v1-bb83f93efd111e042823e53ddfa74c32d81ba74cceca9445dfddfc9e940ff738/bin/samtools: Text file busy So, something is happening too fast I guess, meaning a process is attempting access while this is being created. Any ideas on how I can diagnose this? Not seeing any other errors floating around the logs. Maybe we are dealing with a lustre file locking issue? Thanks, John

2 years, 4 months

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Trackster ownership issue

by Previti

Dear all, I'm having a strange issue with Trackster in our Galaxy implementation. Users seem to be able to upload files ("Add Datasets") from*all *histories of all users, regardless of ownership. ...is this something that has been observed before...? How do I stop this from happening? Thanks and best regards, Christopher -- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661 christopher.previti(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist. Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung. Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.

2 years, 4 months

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V18.01 'View all histories' doesn't work

by Ping Luo

I just installed Galaxy V18.01. I got an error when clicking 'View all histories' in the history tool bar The error says 'The requested URL /api/histories was not found on this server'. Is there anyone experiencing the same problem? Ping

2 years, 4 months

3
5
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galaxy-dev May 2018