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Re: (null):// header in visualisation links (IGV etc.)
by Lubos Klucar 14 Apr '21

14 Apr '21

Dear Helena, thanks a lot, but I'm afraid this is not the case - 'RequestHeader' is set as described. It should be probably some trivial mistake hidden somewhere in the config files, which enable/disable a proper construction of URL text string. I was looking everywhere, but still no luck. best Lubos On 14/04/2021 10:40, Helena Rasche wrote: > Your proxy might not be forwarding the protocol if that's the issue > you're seeing. > > e.g. for apache, https://docs.galaxyproject.org/en/master/admin/apache.html > > # Galaxy needs to know that this is https for generating URLs > RequestHeader set X-URL-SCHEME"%{REQUEST_SCHEME}e" Hope that helps, Ciao > > On 14/04/2021 10:38, klucar(a)embnet.sk wrote: >> When clicking dataset visualisation links (UCSC, IGV, IGB, bam.iobio bam.iobio.io ...) on my galaxy installation [20.09] I'm always getting error: >> >> Error: (null)://mygalaxy.mydomain.org/display_application/3d954174ae8d.... >> >> When manually changing the link from "(null)://" to "https://" the link is fully functional. >> >> Other links from galaxy interface (download icon for any dataset) works without any problems. >> >> Any help would be highly appreciated! >> >> best >> >> Lubos >> ___________________________________________________________ >> 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: >> %(web_page_url)s >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/ -- Lubos Klucar Institute of Molecular Biology Slovak Academy of Science Dubravska cesta 21 845 51 Bratislava 45 Slovakia Tel.: +421 2 5930 7413 Fax.: +421 2 5930 7416

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(null):// header in visualisation links (IGV etc.)
by klucar＠embnet.sk 14 Apr '21

14 Apr '21

When clicking dataset visualisation links (UCSC, IGV, IGB, bam.iobio bam.iobio.io ...) on my galaxy installation [20.09] I'm always getting error: Error: (null)://mygalaxy.mydomain.org/display_application/3d954174ae8d.... When manually changing the link from "(null)://" to "https://" the link is fully functional. Other links from galaxy interface (download icon for any dataset) works without any problems. Any help would be highly appreciated! best Lubos

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April 2021 Galaxy newsletter
by Beatriz Serrano-Solano 13 Apr '21

13 Apr '21

Hello all, This newsletter coincides with the anniversary of James Taylor's death <https://galaxyproject.org/news/2021-04-galaxy-update/#featured-news> on April 2, 2020. James was a Galaxy Project founder and PI, and losing him at the same time as the global COVID-19 shutdown made for a tough month, and then a tough year for the Galaxy Community. To mark this, there are two items about James below. First, *a call to share your favorite story about James* via a 30 second video (by April 30). Second, there is a link to *a note to James* written by project leadership (mainly Anton). The other big news is that registration, abstract submission, and fellowship applications for the 2021 Galaxy Community Conference are now open <https://galaxyproject.org/news/2021-04-galaxy-update/#community-news>. Abstracts and fellowship applications are due by May 7. And as always there are sections on - *upcoming events <https://galaxyproject.org/news/2021-04-galaxy-update/#event-news>*, - news about *public Galaxy platforms <https://galaxyproject.org/news/2021-04-galaxy-update/#galaxy-platforms-news>* , - recent *blog posts <https://galaxyproject.org/news/2021-04-galaxy-update/#galactic-blog-activity>* , - *training and doc updates <https://galaxyproject.org/news/2021-04-galaxy-update/#doc-hub-and-training-…>* , - recent *open-access Galaxy-related publications <https://galaxyproject.org/news/2021-04-galaxy-update/#publications>*, and - *new releases <https://galaxyproject.org/news/2021-04-galaxy-update/#releases>.* It's been a memorable twelve months. It would have been easy to curl up and hide, but we kept going, addressed gaps, and helped address the global pandemic as well. Thanks for supporting each other, Dave Clements and Beatriz Serrano-Solano, Editors

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March 2021 Galaxy Newsletter
by Dave Clements 17 Mar '21

17 Mar '21

Hello all, It is a very busy time in the Galaxy. 2021 is young, but we have already had two large training events, including the largest Galaxy event ever - the GTN Smörgåsbord (with an amazing 1100+ people registered). We are ramping up for GCC2021, which will be online, global, and affordable, and will be more accessible (and likely much larger) than an in-person Galaxy Community Conference. Galaxy is also shifting with the times, and to reflect how our community has grown. This newsletter includes a new *Featured News <https://galaxyproject.org/news/2021-03-galaxy-update/#featured-news>* section highlighting 1) the *recent explosion of videos* related to Galaxy, 2) a draft *global governance model for Galaxy*, and 3) the new *Galaxy Career Center.* That's followed by another new section highlighting *community news <https://galaxyproject.org/news/2021-03-galaxy-update/#community-news>.* Arguably, *everything* here is community news, but items listed here particularly emphasize the community aspects of Galaxy. The newsletter still includes sections on - *upcoming events <https://galaxyproject.org/news/2021-03-galaxy-update/#event-news>*, - news about *public Galaxy platforms <https://galaxyproject.org/news/2021-03-galaxy-update/#galaxy-platforms-news>* , - recent *blog posts <https://galaxyproject.org/news/2021-03-galaxy-update/#galactic-blog-activity>* , - *training and doc updates <https://galaxyproject.org/news/2021-03-galaxy-update/#doc-hub-and-training-…>* , - recent *open-access Galaxy-related publications <https://galaxyproject.org/news/2021-03-galaxy-update/#publications>*, and - *new releases <https://galaxyproject.org/news/2021-03-galaxy-update/#releases>.* It's a lot to take in, but it all highlights the breadth and depth of the Galaxy Community. Enjoy, Dave Clements and Beatriz Serrano-Solano, Editors [image: 2021-03-16_14-51-56-wordcloud.png] -- https://galaxyproject.org/

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Release of Galaxy 21.01
by Marius van den Beek 16 Mar '21

16 Mar '21

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 21.01. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/21.01_announce.html and user facing release notes are at https://docs.galaxyproject.org/en/master/releases/21.01_announce_user.html. A few release highlights are: Workflows: Best Practices, Reports, Invocations ---------------------------------------------------------------- Workflows have seen huge improvements in this release! The workflow report editor is easier than ever to use, providing you with a list of common report components, interactive interfaces for embedding them in your reports, and a new workflow invocation tracker. You can now embed visualizations directly in your workflow reports making summarizing your analyses easier than ever. And, once your reports are produced, you can export them directly to pages to share your reports with colleagues.If you’re building advanced workflows utilizing Galaxy’s powerful sub-workflows for reusable workflow components, then you’ll be pleased to know you can now automatically update those to the latest version Remote Files ------------------ The Remote Files interface is an absolutely fantastic new way to browse your data. Inside Galaxy there is a new, abstract way to reference files locally and on other servers. This lets us provide a uniform interface to FTP servers, your Dropbox, public S3 buckets, and more! You'll find this under Choose Remote Files in the upload interface. This interface is also used for importing and exporting histories. Beta History Panel ------------------------- The History Panel is getting a refresh and a huge performance boost in the latest code. Does this sound exciting to you? Try it out now with the history menu option "Use Beta History Panel". This is not its final state but we'd love feedback from you, the users, on how you find it. It features both performance and usability improvements. E.g. now you can rename files without going into a separate menu, just double click the dataset title! Performance Improvements ------------------------------------- This release includes many performance improvements for browsing and searching Data libraries, improved job creation performance for certain classes of tools and copying Histories, Datasets and Dataset Collections Offload Zip Archive Creation to NGINX --------------------------------------------------- Galaxy can now utilize the NGINX module mod_zip to assemble and compress dataset collection and library dataset archives on the fly. This method is more efficient and can create large archives without affecting the Galaxy server process. The required setup is described in the admin documentation for proxying Galaxy with NGINX. Check out the full release notes <https://docs.galaxyproject.org/en/master/releases/21.01_announce.html> for a lot more details, there are many more enhancements, new visualizations and bug fixes as well as instructions for upgrading your Galaxy installation. Thanks for using Galaxy!

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[GSoC2021] [OGI] Google Summer of Code 2021 is a Go!
by Robin Haw 15 Mar '21

15 Mar '21

Dear All, Sorry for the delay; it was a busy week. The good news is that we’ve been accepted for GSoC 2021. Here’s an update: * Responding to early interest from students. Please watch out for emails! * You can still submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2021>. * Updating the GSoC org page to include new projects. * Setting up the mentors list. * Please send me your preferred email to subscribe you to the mentors list for the group. * To avoid emails being marked as spam please add summerofcode-noreply(a)google.com as a trusted contact. * GSoC timeline - https://summerofcode.withgoogle.com/dashboard/timeline/ * Since we have a few new mentors and projects, I wonder if we could have a meeting to discuss a few things. * Link - https://doodle.com/poll/ukfa9q7xh3pav3nx?utm_source=poll&utm_medium=link Our next landmark date is 29th March, when students can start applying to our organization. Thanks, Robin Robin Haw, PhD Reactome | JBrowse - Senior Project Manager and Outreach Co-ordinator robin.haw(a)oicr.on.ca<mailto:robin.haw@oicr.on.ca> Adaptive Oncology Ontario Institute for Cancer Research MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3 @OICR_news | www.oicr.on.ca<http://www.oicr.on.ca> | @reactome | reactome.org<http://reactome.org> | @JBrowseGossip | jbrowse.org<http://jbrowse.org> Collaborate. Translate. Change lives. This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

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Ansible Galaxy using root user for role installation
by Sandra Maksimovic 17 Feb '21

17 Feb '21

Hi there, Would anyone happen to know why Ansible tries to connect to a remote host (CentOS 7) using 'root' during Galaxy role installation? My playbook has been configured to connect to the remote host using a different user account via SSH, however, the role installation is not honoring this for some reason and continues to use root. The remote host has had SSH root login disabled for security reasons and setting various galaxy user/privsep/become/remote user variables in the group_vars has not had any effect. TASK [galaxyproject.galaxy : Create galaxy_root] * fatal: [server_name]: UNREACHABLE! => {"changed": false, "msg": "Invalid/incorrect password: Permission denied, please try again.\r\nPermission denied, please try again.\r\nroot@server_name: Permission denied (publickey,password).", "unreachable": true} Thanks, Sandra Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

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February 2021 Galaxy Newsletter
by Beatriz Serrano-Solano 08 Feb '21

08 Feb '21

Hi Galaxy Community! The *February 2021 Newsletter <https://galaxyproject.org/news/2021-02-galaxy-update/#event-news>* is out. This time we announce that *GCC2021 goes virtual*, unfortunately. However, this will make it more affordable, and globally accessible to everyone. Other updates include: - *Event news <https://galaxyproject.org/news/2021-02-galaxy-update/#event-news>*: training, webinars, CoFests, conferences... - *Platform news <https://galaxyproject.org/news/2021-02-galaxy-update/#galaxy-platforms-news>*: ATACgraph, corGAT on Laniakea, UseGalaxy.eu - *9 Blog posts <https://galaxyproject.org/news/2021-02-galaxy-update/#galactic-blog-activity>* - *Training material and doc updates <https://galaxyproject.org/news/2021-02-galaxy-update/#doc-hub-and-training-…>*: Admin training, scRNA-seq, videos, new tutorials... - *Publications <https://galaxyproject.org/news/2021-02-galaxy-update/#publications>*: 8 highlights - *Who’s hiring?* <https://galaxyproject.org/news/2021-02-galaxy-update/#whos-hiring> more than 12 open positions - *New releases <https://galaxyproject.org/news/2021-02-galaxy-update/#releases>* - *Other news <https://galaxyproject.org/news/2021-02-galaxy-update/#other-news>* If you have anything to include to next month’s newsletter, then please send it to outreach(a)galaxyproject.org. Thanks for reading, Dave C and Bea

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Nominate a training topic for GCC2021
by Beatriz Serrano-Solano 28 Jan '21

28 Jan '21

Hi all, We are in the process of organizing the Galaxy Community Conference 2021 <https://www.vibconferences.be/events/gcc2021> and we need your input for the training topic nominations. There is a***form* <https://docs.google.com/forms/d/e/1FAIpQLSe-tfL-sD55RQcKU0W4wfglPbcpEZDbuwG…>*that will stay open until the 29th of January*. Please nominate the topics you would like to learn about or present during the training workshops. Thank you very much! Cheers, Bea on behalf of the GCC2021 Organizing Committee

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PaperCuts CoFest Day - Jan 21
by Beatriz Serrano-Solano 18 Jan '21

18 Jan '21

Hi all, We are hosting the Papercuts Day this Thursday all over the day, starting in Australia and finishing in America. Papercuts Day is a collaboration fest to fix minor but annoying bugs in Galaxy (should be doable in one day). These bugs are tagged in different repositories and you can definitely help to find new issues! All the tags, repositories, links to the calls are here: https://galaxyproject.org/events/2021-01-papercuts/ If you are interested in fixing these bugs, or want to learn from the Galaxy developers, please join! Or if you know someone that might be interested, please also encourage them to join :) See you on Thursday! Dave Clements and Beatriz Serrano

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