galaxy-dev March 2018

galaxy-dev@lists.galaxyproject.org

28 participants
26 discussions

How to enable charts visualization for fasta files ?
by SAPET, Frederic 20 Mar '18

20 Mar '18

Hello I would like to enable Multiple Sequence Alignment (BioJS) on fasta file. Right now there is no Charts associated with it (Unfortunately we could not identify a suitable plugin. Feel free to contact us if you are aware of visualizations for this datatype.) How could I do that ? I've tried to dig into tutorial and WIKI (https://galaxyproject.github.io/training-material/topics/dev/tutorials/visu…, https://galaxyproject.org/develop/visualizations/,https://galaxyproject.org…) I'm a bit confused with xml / json files... Do I need to add the datatype in an xml file : <test test_attr="ext" result_type="datatype">txt</test> or in a json config file ? datatypes : [ 'tabular', 'csv' ], I think that after that I will need to rebuild the plugin with mako ? Thank you Fred

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Problems installing Galaxy 18.01
by Peter van Heusden 20 Mar '18

20 Mar '18

Hi there My newly installed Galaxy 18.01 server seems to be unable to install bowtie (the devteam version). I'm documenting my installation progress at: http://pvh.wp.sanbi.ac.za/2018/03/18/galaxy-18-01-install/ As noted in the last paragraph: "My next test was to try and install the bowtie2 tool from the toolshed. This failed, with the tool status going from New to Error with not much interesting left in the logs." The log during the time when I'm trying to install bowtie2 is: 1. [pid: 8856|app: 0|req: 35/48] 10.8.0.2 () {48 vars in 1108 bytes} [Sun Mar 18 19:14:55 2018] GET /admin_toolshed/manage_repository?id=f597429621d6eb2b&operation=install => generated 650 bytes in 26 msecs (HTTP/1.1 302) 3headers in 269 bytes (1 switches on core 1) 2. 10.8.0.2 - - [18/Mar/2018:19:14:57 +0000] "GET /admin_toolshed/manage_repository?id=f597429621d6eb2b&operation=install HTTP/1.1" 302 - " https://galaxy.sanbi.ac.za/admin_toolshed/manage_repository?id=f597429621d6…" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.146 Safari/537.36" 3. [pid: 8856|app: 0|req: 37/49] 10.8.0.2 () {48 vars in 1108 bytes} [Sun Mar 18 19:14:57 2018] GET /admin_toolshed/manage_repository?id=f597429621d6eb2b&operation=install => generated 650 bytes in 24 msecs (HTTP/1.1 302) 3headers in 269 bytes (1 switches on core 0) 4. galaxy.tools.deps DEBUG 2018-03-18 19:14:59,375 [p:8856,w:2,m:0] [ uWSGIWorker2Core2] Dependency bowtie2 not found. 5. galaxy.tools.deps DEBUG 2018-03-18 19:14:59,376 [p:8856,w:2,m:0] [ uWSGIWorker2Core2] Dependency samtools not found. 6. galaxy.tools.deps DEBUG 2018-03-18 19:15:00,028 [p:8856,w:2,m:0] [ uWSGIWorker2Core3] Dependency bowtie2 not found. 7. galaxy.tools.deps DEBUG 2018-03-18 19:15:00,028 [p:8856,w:2,m:0] [ uWSGIWorker2Core3] Dependency samtools not found. 8. 10.8.0.2 - - [18/Mar/2018:19:14:55 +0000] "GET /admin_toolshed/prepare_for_install?changeset_revisions=dc1639b66f12&repository_ids=126c0918b5459666&tool_shed_url=https%3A%2F% 2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 200 - " https://galaxy.sanbi.ac.za/admin_toolshed/manage_repository?id=f597429621d6…" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.146 Safari/537.36" 9. [pid: 8856|app: 0|req: 38/50] 10.8.0.2 () {48 vars in 1274 bytes} [Sun Mar 18 19:14:55 2018] GET /admin_toolshed/prepare_for_install?changeset_revisions=dc1639b66f12&repository_ids=126c0918b5459666&tool_shed_url=https%3A%2F% 2Ftoolshed.g2.bx.psu.edu%2F => generated 19062 bytes in 7001 msecs (HTTP/ 1.1 200) 2 headers in 73 bytes (1 switches on core 2) 10. 10.8.0.2 - - [18/Mar/2018:19:14:57 +0000] "GET /admin_toolshed/prepare_for_install?changeset_revisions=dc1639b66f12&repository_ids=126c0918b5459666&tool_shed_url=https%3A%2F% 2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 200 - " https://galaxy.sanbi.ac.za/admin_toolshed/manage_repository?id=f597429621d6…" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.146 Safari/537.36" 11. [pid: 8856|app: 0|req: 38/51] 10.8.0.2 () {48 vars in 1274 bytes} [Sun Mar 18 19:14:57 2018] GET /admin_toolshed/prepare_for_install?changeset_revisions=dc1639b66f12&repository_ids=126c0918b5459666&tool_shed_url=https%3A%2F% 2Ftoolshed.g2.bx.psu.edu%2F => generated 19062 bytes in 5987 msecs (HTTP/ 1.1 200) 2 headers in 73 bytes (1 switches on core 3) 12. galaxy.tools.toolbox.base DEBUG 2018-03-18 19:15:14,128 [p:8846,w:1 ,m:0] [uWSGIWorker1Core1] Appending to tool panel section: Get Data 13. galaxy.tools.toolbox.base DEBUG 2018-03-18 19:15:14,143 [p:8846,w:1 ,m:0] [uWSGIWorker1Core1] Appending to tool panel section: Get Data 14. 10.8.0.2 - - [18/Mar/2018:19:15:11 +0000] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - " https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_install?changeset_rev…" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.146Safari/537.36" 15. [pid: 8846|app: 0|req: 14/52] 10.8.0.2 () {56 vars in 1329 bytes} [Sun Mar 18 19:15:11 2018] POST /admin_toolshed/prepare_for_install => generated 11133 bytes in 2509 msecs (HTTP/1.1 200) 2 headers in 73 bytes (1 switches on core 1) 16. galaxy.tools.toolbox.base DEBUG 2018-03-18 19:15:15,296 [p:8856,w:2 ,m:0] [uWSGIWorker2Core1] Appending to tool panel section: Get Data 17. 10.8.0.2 - - [18/Mar/2018:19:15:15 +0000] "POST /admin_toolshed/install_repositories HTTP/1.1" 200 - " https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_install" "Mozilla/ 5.0 (X11; Linux x86_64) AppleWebKit/537.36(KHTML, like Gecko) Chrome/65.0 .3325.146 Safari/537.36" 18. [pid: 8856|app: 0|req: 39/53] 10.8.0.2 () {54 vars in 1152 bytes} [Sun Mar 18 19:15:15 2018] POST /admin_toolshed/install_repositories => generated 20 bytes in 206 msecs (HTTP/1.1 200) 2 headers in 73 bytes (1 switches on core 1) 19. 10.8.0.2 - - [18/Mar/2018:19:15:18 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - " https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_install" "Mozilla/ 5.0 (X11; Linux x86_64)AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0 .3325.146 Safari/537.36" 20. [pid: 8856|app: 0|req: 40/54] 10.8.0.2 () {54 vars in 1208 bytes} [Sun Mar 18 19:15:18 2018] POST /admin_toolshed/repository_installation_status_updates => generated 174 bytes in 17 msecs (HTTP/1.1 200) 4 headers in 110bytes (1 switches on core 2) 21. 10.8.0.2 - - [18/Mar/2018:19:15:21 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - " https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_install" "Mozilla/ 5.0 (X11; Linux x86_64)AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0 .3325.146 Safari/537.36" 22. [pid: 8856|app: 0|req: 41/55] 10.8.0.2 () {54 vars in 1208 bytes} [Sun Mar 18 19:15:21 2018] POST /admin_toolshed/repository_installation_status_updates => generated 2 bytes in 14 msecs (HTTP/1.1 200) 4 headers in 110 bytes (1 switches on core 3) 23. 10.8.0.2 - - [18/Mar/2018:19:15:24 +0000] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - " https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_install" "Mozilla/ 5.0 (X11; Linux x86_64)AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0 .3325.146 Safari/537.36" 24. [pid: 8846|app: 0|req: 15/56] 10.8.0.2 () {54 vars in 1208 bytes} [Sun Mar 18 19:15:24 2018] POST /admin_toolshed/repository_installation_status_updates => generated 2 bytes in 27 msecs (HTTP/1.1 200) 4 headers in 110 bytes (1 switches on core 3) which doesn't seem terribly informative. Any ideas? Thanks! Peter

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FileZilla not working
by Antara Biswas 20 Mar '18

20 Mar '18

Dear galaxy team, I am having trouble since a week uploading data from local computer into FileZilla using FTP for transfer to galaxy server. Error message says- connection refused by server. Please help. My login id is ab3(a)nibmg.ac.in Thanks Antara Biswas Research Fellow National Institute of Biomedical Genomics India

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Release of Galaxy 18.01
by Martin Čech 20 Mar '18

20 Mar '18

Dear Galaxy Fans, The release of Galaxy 18.01 is out. Thanks to the Galaxy committers and you, our community! Full release notes: https://docs.galaxyproject.org/en/release_18.01/releases/18.01_announce.html *Highlights:* *Performance and User Experience Improvements* We made Galaxy more lively and responsive. Homepage, published workflows, published/saved histories, and data libraries should all load much faster now. Importing data from FTP will also take less of your time. *Web Server and Configuration* The default web server used by Galaxy has changed from Paste to uWSGI and the default configuration file for Galaxy is now config/galaxy.yml instead of config/galaxy.ini. To minimize the impact of this change on existing Galaxy instances, if a Galaxy has a galaxy.ini file configured, it will continue to use Paste by default unless additional steps are taken by the administrator *Dataset Collection Usability* This release has significantly improved the usability of Galaxy dataset collections. Dozens of improvements to collections have been made, some of the key highlights include: * Data library folders can now be sent to histories as a dataset collection. * Failed dataset collection elements can now be fixed using job re-running * Collections now appear with state and progress bars in the history panel and contained datasets are hidden by default * We added intuitive workflow post job actions for dataset collections * The web interface now supports collections with arbitrary nesting and size * More robust nametag discovery and propagation when using collections *Client Architecture* The architecture for the client code that powers the Galaxy user interface has been significantly overhauled. The code base has been converted to ES6, Yarn now powers the build and dependency management of the code, Prettier is now used to ensure consistent code formatting, and the VueJS framework has been integrated. *New BAM datatypes* Previously Galaxy only supported coordinate sorted BAM files by default (the bam datatype). In addition, this release of Galaxy now supports three new types of BAM: * qname_sorted.bam, that ensures that the file is queryname sorted (e.g. SO:queryname); * qname_input_sorted.bam, that can be used to describe the output of aligners which generally keep mate pairs adjacent * unsorted.bam, that makes no assumptions about the sort order of the file. *Experimental Job Caching* Galaxy can now be configured to allow users the option of skipping duplicated jobs if one with identical parameters has been previously executed and simply reuse the previously generated outputs. Thanks for using Galaxy! http://galaxyproject.org

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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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March Galaxy News: GCCBOSC oral presentations due in 2 weeks, plus lots more
by Dave Clements 16 Mar '18

16 Mar '18

Hello all, The March 2018 Galaxy News <https://galaxyproject.org/galaxy-updates/2018-03/> brings more news than usual, with much of it about upcoming meetings, including GCCBOSC, and continental meetings in Europe and Africa. - *Lots* of GCCBOSC 2018 news <https://galaxyproject.org/galaxy-updates/2018-03/#gccbosc-2018>: - Abstract submission, registration & housing are open <https://galaxyproject.org/galaxy-updates/2018-03/#abstract-submission-regis…> - *Oral presentation abstracts due March 16 <https://easychair.org/conferences/?conf=gccbosc2018>* - Training Schedule set <https://galaxyproject.org/galaxy-updates/2018-03/#training-schedule-set> - 17 topics in 22 sessions over two days covering the full spectrum of open source bioinformatics - We are pleased to announce two of the keynote speakers <http://localhost:8080/galaxy-updates/2018-03/#keynote-speakers>: - Fernando Pérez, of the Berkeley Institute for Data Science, University of California Berkeley and Project Jupyter - Tracy K. Teal, of the Carpentries and the *Journal for Open Scource Software* - Sponsors <https://galaxyproject.org/galaxy-updates/2018-03/#gccbosc-2018-sponsors> : - F1000Research <https://galaxyproject.org/galaxy-updates/2018-03/#f1000research> - Technology Association of Oregon <https://galaxyproject.org/galaxy-updates/2018-03/#technology-association-of…> - Call for sponsors <https://galaxyproject.org/galaxy-updates/2018-03/#call-for-sponsors> - *Continental* community meetings: - *Europe, 14-16 March, Freiburg* <https://galaxyproject.org/galaxy-updates/2018-03/#elixir-galaxy-community-k…> - *Africa, 3-5 April, Cape Town* <https://galaxyproject.org/galaxy-updates/2018-03/#galaxy-africa-3-5-april-c…> - Apply for a Conference Fellowship <https://galaxyproject.org/galaxy-updates/2018-03/#conference-fellowships> *by 10 March*. - Upcoming events <https://galaxyproject.org/galaxy-updates/2018-03/#upcoming-events> (on four continents) - New: - Galactic Blog post from Arun Decano: Coding in the Winter Wonderland: Galaxy Admin Training <https://galaxyproject.org/galaxy-updates/2018-03/#new-galactic-blog-entry-c…> - 133 publications <https://galaxyproject.org/galaxy-updates/2018-03/#publications> (including 5 highlighted ones) - Openings in 6 groups on 2 continents <https://galaxyproject.org/galaxy-updates/2018-03/#whos-hiring> - Public Galaxy Server News <https://galaxyproject.org/galaxy-updates/2018-03/#public-galaxy-server-news> (a new server and two updated ones) - ToolShed contributions <https://galaxyproject.org/galaxy-updates/2018-03/#toolshed-contributions> - Releases <https://galaxyproject.org/galaxy-updates/2018-03/#releases> of Planemo, Pulsar, and galaxy-lib. - And other news <https://galaxyproject.org/galaxy-updates/2018-03/#other-news> too See the newsletter <https://galaxyproject.org/galaxy-updates/2018-03/> for more. Hope to see you in Freiburg, Cape Town, and Portland! Dave C -- https://gccbosc2018.sched.com/ https://galaxyproject.org/ https://usegalaxy.org/

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

14 Mar '18

Dear Mohamed, Following exchanges with Hans and french colleagues as William from the carpem project (university hospital Georges Pompidou), we have finalized a first gie shiny template for Galaxy-E project. You can refer to the GitHub repo for details, don't hesitate to ask more info...https://github.com/65MO/Galaxy-E/tree/master/GIE Cheers,.Yvan Envoyé depuis mon smartphone Samsung Galaxy. -------- Message d'origine --------De : Mohamed Kassam <k.mamoud(a)gmail.com> Date : 14/03/2018 09:59 (GMT+01:00) À : Hans-Rudolf Hotz <hrh(a)fmi.ch> Cc : Yvan Le Bras <yvan.le-bras(a)mnhn.fr>, "Md. Rezaul Karim" <rezaul.karim(a)insight-centre.org>, Timothée VIRGOULAY <timothee.virgoulay(a)mnhn.fr>, Valentin CHAMBON <valentin.chambon(a)mnhn.fr>, Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org> Objet : Re: [galaxy-dev] Shiny in Galaxy Dear all I am contacting about the shiny integration into the Galaxy framewrok. Now, we are running a shiny app outside the Galaxy framework and we are pointing a link in the Galaxy tools that allow the user to open another browser for the use of the shiny app. Howerver we would like to integrate directly the shiny into Galaxy framewrok, and I would like to know if someone find a solution for doing that. Best regards Mohamed 2017-07-11 13:57 GMT+02:00 Hans-Rudolf Hotz <hrh(a)fmi.ch>: Hi Yvan Yes, after an additional week in the South of France, we traveled back safely last weekend. I use the free version of the shiny server. In addition to what you already have mentioned, we run into another 'feature' of the free version: you cannot set the R path. You need to set the R path in the environment of the user, the shiny server is running as. I am currently not using IE, since I cannot use Docker in our production environment. Hence the detour via an html page linking to the extra shiny server. Maybe this will change with Singularity in the future...... Using IE is definitively the way forward. Regards, Hans-Rudolf On 07/06/2017 10:58 PM, Yvan Le Bras wrote: Hi Hans, Hi everyone, I hope your return trip from GCC has been safe! Unfortunately, I didn't take time during gcc to see you Quick and dirty solution... Can we go further on this Shiny / Galaxy integration idea ? It seems that the Shiny licence can be a problem but it appears to me, if I don't make a mistake, that using the open source version of Shiny (without ssl and identification) on Galaxy through IE can be sufficent... no ? Cheers, Yvan ----- Mail d'origine ----- De: Hans-Rudolf Hotz <hrh(a)fmi.ch> À: Yvan Le Bras <yvan.le-bras(a)mnhn.fr>, Md. Rezaul Karim <rezaul.karim(a)insight-centre.org>, Mohamed Kassam <k.mamoud(a)gmail.com>, Timothée VIRGOULAY <timothee.virgoulay(a)mnhn.fr>, Valentin CHAMBON <valentin.chambon(a)mnhn.fr> Cc: Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org> Envoyé: Mon, 29 May 2017 09:39:10 +0200 (CEST) Objet: Re: [galaxy-dev] Shiny in Galaxy Hi Yvan and list This is great news! In my limited spare time, I am currently playing with shiny as well. My current 'quick and dirty' trick goes like this: The galaxy tool creates a new shiny app and the output of the galaxy tool is a html page with the URL to the shiny app. I hope, I will have something ready to show/discuss at GCC Regards, Hans-Rudolf On 05/26/2017 04:13 PM, Yvan Le Bras wrote: 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 <mailto:k.mamoud@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/ <https://lists.galaxyproject.org/> To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/> ___________________________________________________________ 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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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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Error during FASTQ preview
by Previti 13 Mar '18

13 Mar '18

Dear all, I've recently had following error occur on our local Galaxy instance. Every time I want to preview a fastq file it gives this: Content Encoding Error The page you are trying to view cannot be shown because it uses an invalid or unsupported form of compression. Please contact the website owners to inform them of this problem. Any idea how to solve this...? This is the first time I'm seeing it....I tried changing the data type multiple times (fastq, fastq.gz, fastqsanger...etc) but this doesn't get rid of it. Best regards, Christopher Previti -- *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 42-4661 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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API Access and User Impersonation
by John Letaw 13 Mar '18

13 Mar '18

Hi all, We have a system in place that sends jobs to a compute cluster based on the real user name, as opposed to something like ‘galaxyuser’. Galaxy workflows are created and invoked using bioblend code, so the users don’t have to go in and manually set workflow inputs. However, this means each user needs admin access in order to create these workflows via API. Additionally, we have one or two actual admin users that are charged with fixing the occasional workflow problem that pops up. The ability to impersonate users is super helpful in this situation, as you might imagine. So, I’m stuck in this situation where I’d rather not have MOST users with impersonate access. I don’t know of any way to do this, do you? With our setup, can anyone recommend an alternate configuration that would close this security hole? How hard is it to feed a list on email address to the user impersonation config variable? Thanks, John

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galaxy-dev March 2018