job deletion
by Matthias Bernt
Dear list,
i stumbled over a little problem in the implementation of my univa/drmaa
job runner (https://github.com/galaxyproject/galaxy/pull/4857) which
gets its information from qacct. The problem is that jobs that are
deleted before they start are not stored in the job accounting data base
which is used by qacct.
Is there a way to determine that a job was deleted from the Galaxy job
properties? It seems that in the stop_job method of the drmaa runner
does not record anywhere that the job was deleted...
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
-------------------------------------------
3 years, 3 months
galaxy upgrade 18.05 problem
by Matthias Bernt
Dear list,
after upgrading to 18.05 I get an empty page when opening the galaxy
website.
The proxy logs say:
[Mon Jun 11 15:20:10 2018] [error] [client 141.65.5.81] File does not
exist: /data/galaxy_server/galaxy/static/scripts/packed, referer:
https://galaxy.intranet.ufz.de/root/login?redirect=%2F
Which is true, ie. the file/directory does not exist.
Any ideas which step I forgot during the upgrade?
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
-------------------------------------------
3 years, 3 months
Permanently deleting users from a Galaxy instance
by Peter Briggs
Hello
I'm wondering if there is an option to permanently delete a user account from a Galaxy instance, for example to comply with GDPR (for those of us running public Galaxy instances).
The admin interface provides "delete" and "purge" options for user accounts, but neither of these seems to permanently remove an account - the deleted accounts are still visible and can be undeleted (at least, in Galaxy 17.09). It's also unclear to me what "purge" does in this case - I wasn't able to find any documentation on these user management options.
As I understand it, under GDPR a person can request to have all their personal data removed from a database, but neither of the above options would be sufficient to leave the database compliant with GDPR in this case (as at the very least the email address - which I understand constitutes personal information in this context - would remain in the database).
Is there any way within Galaxy to truly permanently remove a user account?
Thanks in advance for any advice on this,
Best wishes
Peter
--
Peter Briggs peter.briggs(a)manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
3 years, 3 months
problem with Visualization 'Scatterplot' in 18.05
by Hans-Rudolf Hotz
Hi all
I am in the process of upgrading our servers to 18.05. And I have
encountered an issue with the Visualization tool "Scatterplot, Creates a
2D-scatterplot from tabular datapoints"
I am starting with a simple bed file for chromosome 15 (downloaded with
UCSC table browser tool). When I click on the Visualization icon,
followed by "Scatterplot", I end up with an near empty page. I only get
the title:
Scatterplot of 'UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)'
UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)
This happens with our development server (after being upgraded from
17.09). It is the same using a new clone of 18.05 code.
It also happens on usegalaxy.eu but it does work on usegalaxy.org
As a side note: on usegalaxy.org, each visualization has its little icon
(see: 'usegalaxy.org.png'), while on usegalaxy.eu, each visualization
just has an eye (see: 'usegalaxy.eu.png')
I hope there is an easy fix for this....
Regards, Hans-Rudolf
--
Hans-Rudolf Hotz, PhD
Bioinformatics Support
Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
3 years, 3 months
Uploads via Nginx proxy fail after upgrade to current release
by Hans-Georg Sommer
Hi,
after updating Galaxy to 18.05 (from 17.05) the file upload doesn't work
anymore, but shows an Internal Server Error (500) in the status column
of the upload form.
We use a nginx proxy also for uploads, configured as described in [1],
galaxy.ini contains the line 'nginx_upload_path = /_upload'.
The nginx access logs show, that the upload requests seem to go to the
wrong location ('/api/uploads' instead of '/_upload'):
0.0.0.0 - - [06/Jun/2018:10:44:43 +0200] "POST /api/uploads HTTP/1.1"
500 193 "https://galaxy.gwdg.de/"
I searched the release notes and the github issues, but wasn't able to
find anything besides [2], which sounds similar but does not give much
information.
Thanks for your help,
Hans-Georg
[1] https://docs.galaxyproject.org/en/latest/admin/nginx.html
[2] https://biostar.usegalaxy.org/p/25870/
--
------------------------------------------------------------------------
Hans-Georg Sommer
Arbeitsgruppe "Anwendungs- und Informationssysteme"
E-Mail: hans-georg.sommer(a)gwdg.de
------------------------------------------------------------------------
Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen
(GWDG)
Am Faßberg 11, 37077 Göttingen, URL: http://www.gwdg.de
Tel.: +49 551 201-1510, Fax: +49 551 201-2150, E-Mail: gwdg(a)gwdg.de
Service-Hotline: Tel.: +49 551 201-1523, E-Mail: support(a)gwdg.de
Geschäftsführer: Prof. Dr. Ramin Yahyapour
Aufsichtsratsvorsitzender: Prof. Dr. Norbert Lassau
Sitz der Gesellschaft: Göttingen
Registergericht: Göttingen, Handelsregister-Nr. B 598
------------------------------------------------------------------------
Zertifiziert nach ISO 9001
------------------------------------------------------------------------
3 years, 3 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
3 years, 3 months
tabular data display
by Matthias Bernt
Dear list,
I'm struggling with tabular data in Galaxy. Attached is a tab separated
file that is generated by MetaProSIP (an updated - not yet committed --
version).
The problem is that it is not shown as table in Galaxy (dev) at all.
Also the peek preview is odd, some values of the header and data are
omitted.
Is this a bug in Galaxy, or of the data in the table?
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
-------------------------------------------
3 years, 3 months