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.
1 year, 10 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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
2 years, 4 months
show tool errors admin interface
by Previti
Dear all,
Does anybody know how to configure galaxy to actually show errors under
the "show tool errors" section of the admin interface?
I can't find any infos about this...we're running version 17.05.
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 42-4434
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, 9 months
Docker Galaxy & HISAT2: ValueError: Parameter index requires a value, but has no legal values defined.
by Peter van Heusden
I'm trying to use HISAT2 using a Docker-ized Galaxy
(bgruening/galaxy-rna-seq:dev - Galaxy 17.05). I installed the HISAT2 index
builder from the toolshed and built an index for the dm3 genome (resulting
in an index in /galaxy-central/tool-data/dm3/hisat2_index/dm3). When I try
and run HISAT2 with this newly created genome, I get the following error:
Traceback (most recent call last):
File "/galaxy-central/lib/galaxy/jobs/runners/__init__.py", line 170, in
prepare_job
job_wrapper.prepare()
File "/galaxy-central/lib/galaxy/jobs/__init__.py", line 878, in prepare
tool_evaluator.set_compute_environment(compute_environment,
get_special=get_special)
File "/galaxy-central/lib/galaxy/tools/evaluation.py", line 72, in
set_compute_environment
visit_input_values(self.tool.inputs, incoming, validate_inputs)
File "/galaxy-central/lib/galaxy/tools/parameters/__init__.py", line 106,
in visit_input_values
visit_input_values(input.cases[values['__current_case__']].inputs,
values, callback, new_name_prefix, label_prefix, parent_prefix=name_prefix,
**payload)
File "/galaxy-central/lib/galaxy/tools/parameters/__init__.py", line 112,
in visit_input_values
callback_helper(input, input_values, name_prefix, label_prefix,
parent_prefix=parent_prefix, context=context)
File "/galaxy-central/lib/galaxy/tools/parameters/__init__.py", line 77,
in callback_helper
new_value = callback(**args)
File "/galaxy-central/lib/galaxy/tools/evaluation.py", line 70, in
validate_inputs
value = input.from_json(value, request_context, context)
File "/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 858, in
from_json
raise ValueError("Parameter %s requires a value, but has no legal
values defined." % self.name)
ValueError: Parameter index requires a value, but has no legal values
defined.
(also at: https://gist.github.com/pvanheus/f463b4a60b064c6f45dd99c1bf883480)
The "index" parameter is the one used in selecting between the genome from
the History and the built-in genome options. Curiously if I spend some time
changing this selection before running the tool the HISAT2 run completes
successfully. This looks like a bug though - any workarounds or suggestions?
Thanks!
Peter
2 years, 9 months
resubmission on out of memory
by Matthias Bernt
Dear list,
I recall that its possible to configure a tool can such that out of
memory conditions (and run time) can be recognized (by regexp matching
on stadout/stderr). Can this be used to trigger job resubmission on the
cluster?
Could someone please point me to some kind of documentation, if this is
the case?
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
-------------------------------------------
2 years, 9 months
Changing $galaxy_lib Variable
by evan clark
Where is it possible to change the $galaxy_lib env variable? We moved
our galaxy instance and this variable we are unable to change the path
to the new location.
2 years, 9 months
Cron Job Tool
by Mohamed Kassam
Dear all,
I made a tool that is doing analysis every two days and send me a
notification by email when the analyis is completed.
I would like to know if I can run this kind of job and how to integrate
this tool in Galaxy tools panel in Galaxy ? If someone has this experience
can help me.
Thanks in advance,
Mohamed
2 years, 9 months
Galaxy server requires a restart to activate tools
by RMSe17
Hello, I have a fresh 17.01 Galaxy installed and set up with uWSGI.
After installing a new tool, I can't run it without first restarting
Galaxy. This is odd, because I know in 17.01 that should no longer be
happening.
The error I get is "This tool was disabled before job completed.
Please contact your Galaxy administrator.
In the logs I see "Tool (... tool name) removed from tool config,
unable to run job
Cleaning up external metadata files
Error checking job readiness"
After Galaxy restarts, the tool runs fine.
Is there anything typical that could cause this? Any place I should
start looking?
Thanks!
2 years, 9 months
Galaxy cloud azur
by Mohamed Kassam
Dear all,
We would like to test Galaxy on the cloud, Did someone had any experience
with the Cloud Azure Microsoft ?
Best regards,
Mohamed
2 years, 9 months
