galaxy-dev September 2017

galaxy-dev@lists.galaxyproject.org

25 participants
22 discussions

Monitoring Dashboard for Galaxy
by evan clark 03 Sep '18

03 Sep '18

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.

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Re: [galaxy-dev] Shiny in Galaxy
by Yvan Le Bras 14 Mar '18

14 Mar '18

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/

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show tool errors admin interface
by Previti 28 Sep '17

28 Sep '17

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.

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Docker Galaxy & HISAT2: ValueError: Parameter index requires a value, but has no legal values defined.
by Peter van Heusden 28 Sep '17

28 Sep '17

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

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Re: [galaxy-dev] upload file format is data - type not recognized in, galaxy
by Evan Clark 27 Sep '17

27 Sep '17

Good afternoon, Which environment file did you modify we are having a similar issue and need to change the $galaxy_lib environment variable. galaxy-dev-request(a)lists.galaxyproject.org wrote: > Re: upload file format is data - type not recognized in > galaxy

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resubmission on out of memory
by Matthias Bernt 27 Sep '17

27 Sep '17

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 -------------------------------------------

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Changing $galaxy_lib Variable
by evan clark 26 Sep '17

26 Sep '17

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.

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Cron Job Tool
by Mohamed Kassam 26 Sep '17

26 Sep '17

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

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Galaxy server requires a restart to activate tools
by RMSe17 26 Sep '17

26 Sep '17

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!

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Galaxy cloud azur
by Mohamed Kassam 26 Sep '17

26 Sep '17

Dear all, We would like to test Galaxy on the cloud, Did someone had any experience with the Cloud Azure Microsoft ? Best regards, Mohamed

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galaxy-dev September 2017