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, 11 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, 2 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
3 years, 2 months
tool dependencies
by Matthias Bernt
Hi all,
I tried to install velvetoptimizer (for the assembly tutorial in the GTN).
It lists velvetoptimiser as requirement in the main xml and the
tool_dependencies.xml (listing the installation steps). Now there seems
to be a conda package perl-velvetoptimiser.
What would be the steps to to update the tool (I would happily create a
PR)? Is the tool_dependencies.xml intended to be kept and I just need to
update the names of the requirements (I guess the name in the
tool_dependencies.xml does not matter)?
Furthermore the tool_dependencies.xml includes the package_velvet which
is listed as missing dependency in the management pages. Shouldn't this
be ignored if there is a conda package?
Last question: Is it possible to update an installed package by editing
the xml files? It seemed to me that changes do not have an effect.
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, 4 months
Re: [galaxy-dev] Shiny in Galaxy
by Yvan Le Bras
Dear Mohamed, Karim, galaxy-dev list,
A rapid e-mail to inform you that we plan to work on this task in the upcoming weeks with Thimothée and Valentin, copied. We have had some exchanges with Eric (Rasche) and Björn (Grüning) and it seems that using the Galaxy "interactive environment" functionality is a good way to proceed. Don't hesitate to give us more informations to collaborate on it...
Wishing you a good week end.
Cheers,
Yvan
-------- Message d'origine --------
De : "Md. Rezaul Karim" <rezaul.karim(a)insight-centre.org>
Date : 26/05/2017 15:45 (GMT+01:00)
À : Mohamed Kassam <k.mamoud(a)gmail.com>
Cc : Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org>
Objet : Re: [galaxy-dev] Shiny in Galaxy
+1
On May 26, 2017 2:44 PM, "Mohamed Kassam" <k.mamoud(a)gmail.com> wrote:
Dear all,
I have a shiny application working in my RStudio, but I would like to integrate it to Galaxy that the users can call my application via Galaxy .
Thanks in Advance,
Mohamed
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3 years, 4 months
bigwig problem
by Jochen Bick
Hi,
how can I fix this problem?
bedGraphToBigWig: error while loading shared libraries: libmysqlclient.so.18: cannot open shared object file: No such file or directory
I have the files in the local bin but somehow it does not work inside galaxy.
Thanks in advance.
Cheers
Jochen
3 years, 5 months
Updating Bioblend on existing Galaxy installation
by Lachlan Musicman
Hola,
I've just noticed that our Galaxy 17.09 installation has Bioblend 0.9
installed, and that one of the changes in Bioblend 0.10 was "support for
galaxy 17.09".
Can someone hip me to the easiest way to update bioblend?
Is it just to activate the venv and pip install -U bioblend?
Cheers
L.
------
"The antidote to apocalypticism is *apocalyptic civics*. Apocalyptic civics
is the insistence that we cannot ignore the truth, nor should we panic
about it. It is a shared consciousness that our institutions have failed
and our ecosystem is collapsing, yet we are still here — and we are
creative agents who can shape our destinies. Apocalyptic civics is the
conviction that the only way out is through, and the only way through is
together. "
*Greg Bloom* @greggish
https://twitter.com/greggish/status/873177525903609857
3 years, 5 months
environment for jobs
by Matthias Bernt
Dear list,
there seem to be two ways to setup an environment for jobs:
- in galaxy.ini: variable environment_setup_file
- in job_conf.xml: <env> tag in the destinations
I'm wondering what the rationale is behind these two options?
Is it to setup special environments for each destination?
I guess that both should be loaded in each job. But in which order?
I guessed that the file given in the <env> tag is sourced in the job
submit scripts, but this seems to happen not for all jobs...?
Best,
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, 5 months
GCCBOSC 2018 Abstract Submission & Early Registration are Open
by Dave Clements
Hello all,
We are pleased to announce that abstract submission and early registration
for GCCBOSC2018 <https://gccbosc2018.sched.com/> are now open.
- Submit an abstract
<https://easychair.org/conferences/?conf=gccbosc2018> (oral presentation
abstracts due March 16)
- Register <https://gccbosc2018.eventbrite.com/>
- Book conference housing <https://gccbosc2018housing.eventbrite.com/>
GCCBOSC 2018 <https://gccbosc2018.sched.com/> will be held 25-30 June in
Portland, Oregon, United States. This brings the 2018 Galaxy Community
Conference and the Bioinformatics Open Source Conference together into a
unified week-long event. If you work in open source life science or
data-intensive biomedical research, then there is no better place than
GCCBOSC 2018 to present your work and to learn from others.
Events
GCCBOSC <https://gccbosc2018.sched.com/> starts with two days of training
<https://gccbosc2018.sched.com/overview/type/C.x+Training+-+All> with a
wide range of topics nominated and selected by our communities. Training is
followed by a two day meeting, with joint and parallel tracks, featuring
oral presentations, posters, demos, lightning talks,
birds-of-a-feather and invited
keynotes <https://galaxyproject.org/events/gccbosc2018/keynotes/>from Fernando
Pérez
<https://galaxyproject.org/events/gccbosc2018/keynotes/#bosc-gcc-joint-key...>
of the Berkeley Institute for Data Science <https://bids.berkeley.edu/> and
Project Jupyter <http://jupyter.org/>, and Tracy K. Teal
<https://galaxyproject.org/events/gccbosc2018/keynotes/#bosc-2018-keynote-...>
of The Carpentries. The week finishes with *CollaborationFest
<https://galaxyproject.org/events/gccbosc2018/collaboration/> Core* and
*Encore*, two or four days of collaborative work on code, documentation,
training and challenging data analysis problems.
Abstract Submission
BOSC and GCC are now accepting abstracts
<https://easychair.org/conferences/?conf=gccbosc2018> for oral
presentations, posters, demos, and lightning talks. We are using EasyChair
<https://easychair.org/> for submissions. If you don't already have an
account, you'll need to create one.
*The deadline for oral presentations is rapidly approaching (March 16) so
plan to submit your abstracts soon.*
Registration
Register now <https://gccbosc2018.eventbrite.com/> to take full advantage of
early registration discounts
<https://galaxyproject.org/events/gccbosc2018/register/> for
students/post-docs (75% off full price), non-profits (67%) and industry
(50%). Early registration rates for students and post-docs average $66 /
day.
Conference Housing
Official conference housing <https://gccbosc2018housing.eventbrite.com/> for
GCCBOSC 2018 is in Reed residence halls. Rooms are within easy walking
distance of all conference venues. Room prices per night drop the longer
the stay. If you prefer to stay elsewhere, Reed College has a list of
recommended hotels <https://www.reed.edu/accommodations.html>, many
offering a discount for those attending events at Reed.
Travel Fellowships
Both OBF and the Galaxy Community Fund Board are offering fellowships to
attend GCCBOSC 2018:
- OBF Travel Fellowships
<https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md>,
deadline is April 15.
- GCC2018 Fellowships
<https://galaxyproject.org/news/2018-02-20-gcc-fellowships/>, first
deadline is March 16.
See you in Portland!
The GCCBOSC 2018 Organizers
<https://galaxyproject.org/events/gccbosc2018/organizers>
--
https://galaxyproject.org/
https://usegalaxy.org/
3 years, 5 months
Help with from_dataset param in Galaxy XML
by SAPET, Frederic
Hello
I try to use the from_dataset param.
I have a tabular file with two columns : sequence and ids
I would like to let users select some sequences, based on the ids.
<param name="seq" type="select" size="120" optional="false" multiple="true" label="Choose your sequences">
<options from_dataset="target">
<column name="name" index="1"/>
<column name="value" index="0"/>
</options>
</param>
But I would like to be able to access not only the sequences data, but also the ids.
In the <command> tag :
name=$seq.name : it give me "seq", the name of my parameter
value=$seq.value : it gives me "atcgatcga,tagctacgatcg,aatctactacta", that's fine.
I would like to print the id of each sequence.
Is it possible ?
Thank you.
Fred
---
Frederic Sapet
Bioinformatics Research Engineer
BIOGEMMA - Upstream Genomics Group
Centre de Recherche de Chappes
CS 90126
63720 CHAPPES
FRANCE
Tel : +33 (0)4 73 67 88 54
Fax : +33 (0)4 73 67 88 99
E-mail : frederic.sapet(a)biogemma.com<mailto:frederic.sapet@biogemma.com>
3 years, 5 months
