galaxy-dev April 2021

galaxy-dev@lists.galaxyproject.org

5 participants
6 discussions

[GSoC2021] [OGI] Participation in Google Summer of Code 2021
by Robin Haw 15 Mar '22

15 Mar '22

Dear All, The Open Genome Informatics team serves as an “umbrella" organization to support the efforts of many open-access open-source bioinformatics projects for <https://summerofcode.withgoogle.com/> Google Summer of Code (GSoC<https://summerofcode.withgoogle.com/>). Among this list of projects are Reactome and GMOD and its software projects -- JBrowse; Galaxy; WormBase; and others. Call for 2021 Project Ideas and Mentors: We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2021>. For more information please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC><http://gmod.org/wiki/GSoC#Google_Summer_of_Code_2020>. The mentoring organization application deadline with GSoC is February 19th at 2 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible. Please forward this to others who might be interested in taking part. If you have any questions please let us know. Thanks, Robin, Marc, and Scott.

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Share your favorite James Taylor Story
by Dave Clements 27 Apr '21

27 Apr '21

Hi All, In case you missed this <https://galaxyproject.org/news/2021-04-jxtx-videos/> on other channels, the deadline is this week: It's been a year since James Taylor <https://galaxyproject.org/jxtx/> passed away. To remember him, and mark his upcoming birthday (May 18) we would like to create a community video. We are asking you to tell us your favorite story about James in ~ 30 seconds. We will combine your clips into a community video that will be prominently featured on all Galaxy-related sites. Here is what we will need you to do before April 30: 1. Think of your favorite story/interaction/event involving James. 2. Pick a nice location and record the video! 3. The video should be: - in a high-resolution - without background noise - in a horizontal orientation (not vertical!) - ≲ 30 seconds in length 4. Deposit video file to your Google Drive or Dropbox folder (or any other location that would allow us to retrieve it) 5. Send a link to the video, your name and location as you would like them to appear in the final video to: outreach(a)galaxyproject.org Thank you all in advance and please feel free to send this to other friends of James. Galaxy Outreach -- https://galaxyproject.org/

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Custom Galaxy auth provider
by Matthieu DANIEL 23 Apr '21

23 Apr '21

Hello all, We are currently installing our first galaxy instance and very happy with. But for security needs, we must implement our auth provider. It is very similar to the ldap auth provider but need to get ip information to match specific information from specific database. Is there a simple way to have the IP of the user who's logging in the web portal directly accessible from the python provider code ? Thank you for all the answers ! Best, Matth

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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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galaxy-dev April 2021