Monitoring Dashboard for Galaxy
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, 8 months
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, 11 months
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, 11 months
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, 11 months
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, 11 months
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, 11 months
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, 11 months
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, 11 months
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, 11 months
