- galaxy-dev - lists.galaxyproject.org

FTP service for galaxy with external authentication via SAML using shibboleth
by Martin Demko 17 Apr '18

17 Apr '18

Hi, I'm currently solving a problem with authentication to FTP service for users of our galaxy server. We've successfully established an authentication via shibboleth behind Nginx (not very easy, but doable :) but that also means that ProFTPD is not working anymore, as it doesn't support SAML authentication. So my question is obvious, I'm looking for an easy and free FTP server with SAML support, can anybody help me with an advice? I've already found CompleteFTP and CrushFTP but both are paid and one is Windows-only allegedly. So how do you - people using external authentication via SAML - do this? Thanks in advance for any kind of useful advice. Best wishes, Martin Demko

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planemo/toolshed error, assistance request
by Dennis, H. E. Cicada Brokaw 13 Apr '18

13 Apr '18

Hello, I am having a problem using planemo to upload a suite of tools into the testtoolshed. The tools at this point are all in the toolshed from using the shed_create and shed_update commands in the suite directory. However, along the way there were some errors in uploading some of the tools that I had to fix. Those are all fixed and all the tools show as up to date, except for the suite, which is returning the following error message, about which I have no idea what to do (and I have tried a lot of different things): The repository_dependencies.xml file contains an invalid <repository> tag. Invalid latest installable changeset_revision 000000000000 retrieved for repository ctat_metagenomics owned by trinity_ctat. Does anyone have an idea of what to do to fix this? Thanks, Cicada Dennis

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Doubts about FTP upload.
by Álvaro Rios 11 Apr '18

11 Apr '18

Dear I am trying to upload files via FTP. However, the following message appears. "Authentication required ftp://usegalaxy.org Your connection to this site is not private." I do not have the experience to use galaxy, What I need to do? Thank you. Álvaro Rios.

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April Galactic News: UseGalaxy.org gets some siblings, GCCBOSC and other event news; new pubs, servers, jobs, ...
by Dave Clements 11 Apr '18

11 Apr '18

Hello all, The April 2018 Galactic News <https://galaxyproject.org/galaxy-updates/2018-04/> highlights what's going on in the Galaxy (and it's actually quite cool). Take a look: - *UseGalaxy.eu and UseGalaxy.org.au Launched <https://galaxyproject.org/galaxy-updates/2018-04/#usegalaxyeu-and-usegalaxy…>* - Lots of GCCBOSC 2018 news <https://galaxyproject.org/galaxy-updates/2018-04/#gccbosc-2018>: - We are pleased to announce that Lucia Peixoto <https://galaxyproject.org/galaxy-updates/2018-04/#keynote-speakers> of Washington State University will be our third keynote speaker. - Please welcome *Google Cloud <https://galaxyproject.org/galaxy-updates/2018-04/#google-cloud>* as a GCCBOSC Platinum sponsor. - *GCC Lightning talk, poster and demo submissions are due by April 16 <https://galaxyproject.org/galaxy-updates/2018-04/#submit-gcc-lightning-talk…>* - Childcare for GCCBOSC <https://galaxyproject.org/galaxy-updates/2018-04/#childcare-at-gccbosc>! Space is limited, so register *now*. - Upcoming Events: - 2018 Big Genomics Data Skills Training course <https://galaxyproject.org/galaxy-updates/2018-04/#2018-big-genomics-data-sk…> - how to integrate genomic data analysis into undergraduate coursework - Gateways 2018 Call for Participation <https://galaxyproject.org/galaxy-updates/2018-04/#gateways-2018-call-for-pa…> - Upcoming events <https://galaxyproject.org/galaxy-updates/2018-04/#upcoming-events> (on four continents) - New: - 119 publications <https://galaxyproject.org/galaxy-updates/2018-04/#publications> (including 9 highlighted ones) - Openings in 9 groups on 2 continents <https://galaxyproject.org/galaxy-updates/2018-04/#whos-hiring> - Public Galaxy Server News <https://galaxyproject.org/galaxy-updates/2018-04/#public-galaxy-server-news> (a new server and an updated one too) - ToolShed contributions <https://galaxyproject.org/galaxy-updates/2018-04/#toolshed-contributions> - Releases <https://galaxyproject.org/galaxy-updates/2018-04/#releases> of Galaxy, Galaxy Docker, blend4j, and galaxy-lib - And other news <https://galaxyproject.org/galaxy-updates/2018-04/#other-news> too See the newsletter <https://galaxyproject.org/galaxy-updates/2018-04/> for the full story, and we hope to see you in Portland! Dave C, on behalf of the Galaxy -- https://gccbosc2018.sched.com/ https://galaxyproject.org/ https://usegalaxy.org/

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question regarding GALXY software
by דויד קורנספן [David Kornspan] 10 Apr '18

10 Apr '18

Hi, I would appreciate your advice regarding the recommended portable computer specifications which will enable running the GALXY software for analysis of DNA and RNA seq of bacterial genomes. Thanks, David Kornspan

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Ballgown does not work
by Jochen Bick 10 Apr '18

10 Apr '18

Hi, I'm trying to install Ballgown but it throws some error message after running it: cannot find 'dataset' while searching for 'param_name.dataset.dataset' the script does not have test-data file and it also does not install the requirements. Cheers Jochen

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Problems running reporting app with reports.yml using --daemon
by Peter Briggs 28 Mar '18

28 Mar '18

Dear devs I'm trying to update my ansible playbooks for deploying Galaxy and I'm having problems when trying to run the reporting app in release_17.09 using a 'reports.yml' file (rather than 'reports.ini'), when specifying the --daemon option. Running without any arguments, the application appears to start okay - but if I do sh ./run_reports.sh --daemon then it exits with the error: /XXXXX/galaxy/.venv/bin/python: unrecognized option '--safe-pidfile' getopt_long() error This seems to be coming from the invocation of uwsgi within the run_reports.sh script, and looks like an issue with Galaxy's version of uWSGI: version 2.0.15 (as specified in the requirements.txt file) doesn't support the '--safe-pidfile' option (that needs uWSGI 2.0.16). Editing requirements.txt to use 2.0.16 seems to address this issue (as in, --daemon no longer fails on startup). Has anyone else encountered this issue? My ultimate goal is to be able to serve the uwsgi-based reports app via an nginx proxy (which used to work with the old i.e. non-uwsgi reports.ini-configured version). Thanks for your help, Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Tool to download galaxy datasets locally
by evan clark 27 Mar '18

27 Mar '18

Has anyone attempted to write a tool that allows copying of galaxy datasets locally, i.e. without downloading via http. We have scenario where there are some additional tools available only via command line and it would be very useful to be able to directly copy galaxy datasets from the datasets folder.

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Re: [galaxy-dev] Shiny in Galaxy
by Romain Dallet 27 Mar '18

27 Mar '18

Dear Mohamed, Karim, Hans, I don't know if you are still looking for a Galaxy Interactive Environment with Shiny. But in collaboration with Yvan's team, we have also developed a generic Shiny GIE for the Workflow4Metabolomics project. You can find it with an example on GitHub at the following link : https://github.com/workflow4metabolomics/gie-shiny . If you find mistakes or something require more informations in the tutorial, don't hesitate to make a pull request and if you have some questions, please, ask me. Romain and Gildas >> Début du message réexpédié : >> >> *De: *Yvan Le Bras <yvan.le-bras(a)mnhn.fr <mailto:yvan.le-bras@mnhn.fr>> >> *Objet: **Rép : [galaxy-dev] Shiny in Galaxy* >> *Date: *14 mars 2018 à 10:14:14 UTC+1 >> *À: *Mohamed Kassam <k.mamoud(a)gmail.com <mailto:k.mamoud@gmail.com>>, >> Hans-Rudolf Hotz <hrh(a)fmi.ch <mailto:hrh@fmi.ch>> >> *Cc: *Timothée VIRGOULAY <timothee.virgoulay(a)mnhn.fr >> <mailto:timothee.virgoulay@mnhn.fr>>, Galaxy Dev List >> <galaxy-dev(a)lists.galaxyproject.org >> <mailto:galaxy-dev@lists.galaxyproject.org>>, Valentin CHAMBON >> <valentin.chambon(a)mnhn.fr <mailto:valentin.chambon@mnhn.fr>> >> >> 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 <mailto:k.mamoud@gmail.com>> >> Date : 14/03/2018 09:59 (GMT+01:00) >> À : Hans-Rudolf Hotz <hrh(a)fmi.ch <mailto:hrh@fmi.ch>> >> Cc : Yvan Le Bras <yvan.le-bras(a)mnhn.fr >> <mailto:yvan.le-bras@mnhn.fr>>, "Md. Rezaul Karim" >> <rezaul.karim(a)insight-centre.org >> <mailto:rezaul.karim@insight-centre.org>>, Timothée VIRGOULAY >> <timothee.virgoulay(a)mnhn.fr <mailto:timothee.virgoulay@mnhn.fr>>, >> Valentin CHAMBON <valentin.chambon(a)mnhn.fr >> <mailto:valentin.chambon@mnhn.fr>>, Galaxy Dev List >> <galaxy-dev(a)lists.galaxyproject.org >> <mailto:galaxy-dev@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 >> <mailto:hrh@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 <mailto:hrh@fmi.ch>> >> À: Yvan Le Bras <yvan.le-bras(a)mnhn.fr >> <mailto:yvan.le-bras@mnhn.fr>>, Md. Rezaul Karim >> <rezaul.karim(a)insight-centre.org >> <mailto:rezaul.karim@insight-centre.org>>, Mohamed Kassam >> <k.mamoud(a)gmail.com <mailto:k.mamoud@gmail.com>>, Timothée >> VIRGOULAY <timothee.virgoulay(a)mnhn.fr >> <mailto:timothee.virgoulay@mnhn.fr>>, Valentin CHAMBON >> <valentin.chambon(a)mnhn.fr <mailto:valentin.chambon@mnhn.fr>> >> Cc: Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org >> <mailto:galaxy-dev@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 >> <mailto:rezaul.karim@insight-centre.org>> >> Date : 26/05/2017 15:45 (GMT+01:00) >> À : Mohamed Kassam <k.mamoud(a)gmail.com >> <mailto:k.mamoud@gmail.com>> >> Cc : Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org >> <mailto:galaxy-dev@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> >> <mailto:k.mamoud@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/> >> <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/> >> <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/ >> <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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GVL/Galaxy ver 18.01 instance error: R_COMM channel basic get exception: [Errno 32] Broken pipe
by Leon Parker 26 Mar '18

26 Mar '18

We just stood up our first ever Genomics Virtual Lab appliance and used it to spool up a Galaxy Cluster for doing bioinformatics work. We’ve worked a bit with the original “Cloudman” application and the ver 17.05 revision of Galaxy and it has worked fine, but we decided it might be a good time to migrate the GVL platform because it uses the latest, greatest version of Galaxy and provides additional tools, and the old “cloud man” approach has been deprecated, giving us further incentive to make the switch. Unfortunately, we’re encountering an error right out of the gate, when we spool up Galaxy through GVL, before we do anything with it. Within two minutes of Galaxy starting, we begin to see the following over and over again in the Cluster Info Log: 20:55:20 - R_COMM channel basic get exception: [Errno 32] Broken pipe In addition, we can’t seem to access any Spot worker node instances we activate. They launch but are never recognized and used. Not sure what this mean, as we are biologists, not informaticians nor python experts. Any help would be most appreciated! --Leon

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