December 2017 - galaxy-dev - lists.galaxyproject.org

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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Job Script Integrity
by John Letaw 04 Jun '18

04 Jun '18

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

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tool dependencies
by Matthias Bernt 19 Mar '18

19 Mar '18

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

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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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Galaxy v17.09 impersonation doesn't work
by Ping Luo 20 Dec '17

20 Dec '17

The impersonation feature in Galaxy v17.09 doesn't work as expected. After clicking the person to impersonate, the webpage shows "you have now logged in as xxx, return to home page', where 'xxx' is the name of the person I want to impersonate. So far so good. But after I click home, and check the login information, the login name is still myself. Is there anything I missed in the configuration file? Thanks, Ping

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tool publishing
by Matthias Bernt 18 Dec '17

18 Dec '17

Dear dev-list, I'm just trying to publish my first tool to the testtoolshed via planemo. I got some problem during the process. Maybe someone can kickstart me (I guess I just forgot something). I followed http://planemo.readthedocs.io/en/latest/publishing.html The step `planemo shed_create --shed_target testtoolshed` ``` Repository created cd '/home/berntm/projects/mb-galaxy-tools/fasta_regex_finder' && git rev-parse HEAD cd '/home/berntm/projects/mb-galaxy-tools/fasta_regex_finder' && git diff --quiet Repository [fasta_regex_finder] does not exist in the targeted Tool Shed. ``` When I check online the repository is there but no changeset seems available. Retrying fails (expected): `planemo shed_create --shed_target testtoolshed` ``` Unexpected HTTP status code: 400: {"err_msg": "You already own a repository named <b>fasta_regex_finder<\/b>, please choose a different name.", "err_code": 400008} ```` Also shed_diff fails `fasta_regex_finder git:(master) ✗ planemo shed_diff --shed_target testtoolshed` ``` shed_diff: Repository [fasta_regex_finder] does not exist in the targeted Tool Shed. ``` Any idea? 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 -------------------------------------------

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intended behaviour for multiple data sets
by Matthias Bernt 18 Dec '17

18 Dec '17

Dear list, In addition to single datasets tool file inputs allow to choose between - multiple dataset - dataset collection - some tools use repeat tags for multiple inputs I would like to know what the intended behavior of galaxy is for the three options considering multiple datasets? Is this described somewhere? Is it that the tool is applied to each of the multiple inputs separately or at once. For some tools one case makes more sense than the other. 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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GCCBOSC 2018 Training Topic Nominations are Open!
by Dave Clements 14 Dec '17

14 Dec '17

Hello all, This email in 5 words: *Nominate a training topic now <http://bit.ly/gccbosc2018-tr-nom>!* Or, the longer version: The joint 2018 Galaxy Community and Bioinformatics Open Source Conferences <https://gccbosc2018.sched.com/> start with training and *the training topics are determined by you*. Please take a few minutes to consider what you would like to learn (or teach) at GCCBOSC2018. Any topic(s) of interest to these communities can be *nominated <http://bit.ly/gccbosc2018-tr-nom>.* GCCBOSC2018 <https://gccbosc2018.sched.com/> will be held 25-30 June in Portland, Oregon, United States, and will feature two days of training - the second of which is multi-track and will feature content for both the BOSC and Galaxy communities. Nominations can cover a wide range of topics. For example: - How to use open source software using just a web browser (e.g., Intro to Using Galaxy) - How to use software packages (The Newbie's Guide to BioRuby) - Advanced applications of software (Genome Assembly with Galaxy, or Proteomics with BioPython) - Software installation and configuration (Tool Wrapping for Galaxy, or Using CloudLaunch) - Open source community (Building a Curation Community using Apollo, or Training using the Galaxy Training Network) *These are only examples.* If you are looking for ideas, see topics nominated for GCC2017 <https://docs.google.com/document/d/1jyCndVqfXx-HsyFJ4hjaK075vDbPM1kE58qO2lJ…> , GCC2016 <http://bit.ly/gcc2016noms>, GCC2015 <http://bit.ly/gcc2015vote>, and the Galaxy Events page <https://galaxyproject.org/events/>, which lists what training the community is offering outside of GCCs. *Training is not limited to Galaxy-related topics. Don't be afraid to think inside the BOSC!* Basically, if you think our communities will be interested in a topic, then please nominate it <http://bit.ly/gccbosc2018-tr-nom>! Nominated topics will be published <https://galaxyproject.org/events/gccbosc2018/training/> as they come in. *Topic Nominations close January 7*. Topics will be compiled into a uniform list by the GCCBOSC2018 organizers, and then voted on by the community starting one week later. Looking forward to seeing you in Portland! Dave Clements, on behalf of the GCCBOSC 2018 Organizers -- https://galaxyproject.org/ https://usegalaxy.org/

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History Share : options
by Christophe Caron 14 Dec '17

14 Dec '17

Hi When a user wants to share a history ti a user, it seems the are several use cases after validation. In some cases, no question and the history is shared, but in some other use cases Galaxy request more informations with one, two or three questions (list below). 1/ Make datasets public so anyone can access them ? 2/ Make datasets private to me and the user(s) with whom I am sharing ? 3/ Share Anyway ? We try to identify the source of these different proposals. It seems to be link with role and dataset owner ...but not sure. Any advice or clue ? Is there any documentation of potential links between these options end user roles ? Thanks Christophe Thanks

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Network errors when downloading files
by William, Van Der Pol 14 Dec '17

14 Dec '17

Hello, We've noticed when our users try to download files from our galaxy instance, they are getting a network error and receiving an empty 0 Byte file. I've checked the directory where the datasets are stored and can see that the files in question exist and contain the expected data, but something is interfering with downloading them through the GUI. Do you guys have any suggestions on what could be causing this error? Thanks -Liam Help keep the CCTS funded. Please include the following text on relevant publications: "This publication was made possible by the UAB Center for Clinical and Translational Science Grant Number UL1TR001417 from the National Center for Advancing Translational Sciences (NCATS) of the National Institutes of Health (NIH)."

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