galaxy-dev February 2018

galaxy-dev@lists.galaxyproject.org

15 participants
19 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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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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Text file busy and conda
by John Letaw 16 May '18

16 May '18

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

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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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bigwig problem
by Jochen Bick 06 Mar '18

06 Mar '18

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

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Updating Bioblend on existing Galaxy installation
by Lachlan Musicman 22 Feb '18

22 Feb '18

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

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environment for jobs
by Matthias Bernt 21 Feb '18

21 Feb '18

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

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GCCBOSC 2018 Abstract Submission & Early Registration are Open
by Dave Clements 20 Feb '18

20 Feb '18

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-keyno…> 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-tr…> 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/

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Help with from_dataset param in Galaxy XML
by SAPET, Frederic 20 Feb '18

20 Feb '18

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>

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galaxy-dev February 2018