galaxy-dev May 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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June 2021 Galaxy Newsletter: All about GCC2021!
by Beatriz Serrano-Solano 31 May '21

31 May '21

Hello all, Welcome to the June 2021 edition of Galaxy News. GCC2021 is upon us, *with deadlines and events starting this month <https://galaxyproject.org/news/2021-06-galaxy-update/#featured-news>*. It's not too late to register (register by June 8 and get 50% off) and to submit Poster/Demo abstracts. Training week starts on June 28. We also started getting confirmations from speakers and are *publishing confirmed presenters <https://galaxyproject.org/news/2021-06-galaxy-update/#featured-news>* as we get them. We are also pleased to *announce our first three sponsors for GCC2021: F1000Research, GigaScience Press and KWS-SAAT <https://galaxyproject.org/news/2021-06-galaxy-update/#gcc2021-sponsorships>* . In addition to GCC news, we also released the *James Taylor birthday video <https://galaxyproject.org/news/2021-06-galaxy-update/#community-news>*, and have several *new open positions <https://galaxyproject.org/news/2021-06-galaxy-update/#community-news>*, lots of *event news <https://galaxyproject.org/news/2021-06-galaxy-update/#event-news>*, *Galaxy platform news <https://galaxyproject.org/news/2021-06-galaxy-update/#galaxy-platforms-news>*, *Galactic blog posts <https://galaxyproject.org/news/2021-06-galaxy-update/#galactic-blog-activity>*, *training and doc updates <https://galaxyproject.org/news/2021-06-galaxy-update/#doc-hub-and-training-…>*, recent *open-access Galaxy-related publications <https://galaxyproject.org/news/2021-06-galaxy-update/#publications>*, and *new releases <https://galaxyproject.org/news/2021-06-galaxy-update/#releases>.* As always, thanks for using Galaxy, Dave Clements and Beatriz Serrano-Solano, Editors PS: Subscribe to the Galaxy Announce mailing list <https://lists.galaxyproject.org/?count=100&all-lists=> to receive an email whenever this newsletter is published. -- Dr Beatriz Serrano-Solano (she/her) <https://www.hrc.org/resources/talking-about-pronouns-in-the-workplace> Bioinformatics Group Dept. Computer Science Albert-Ludwigs-Universität Freiburg Georges-Köhler-Allee, 106 70110 Freiburg Germany

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Webinar, Wednesday May 26: Galaxy Resources for Admins and Infrastructure Providers
by Dave Clements 25 May '21

25 May '21

Hello all, We are closing the webinar series *"Galaxy Resources for..."* tomorrow with > Gianmauro Cuccuru and Lucille Delisle. They will talk about the relevant > resources for *Galaxy admins and infrastructure providers*. Please feel > free to register and share this link: > > https://galaxyproject.org/events/2021-05-gr4-admins/ > We hope to see you there, Dave "Blatantly copying Beatriz Serrano-Solano who reminded me to post this here" C PS: Also, some GCC2021 news. The early registration deadline for GCC2021 is Monday, June 1. We may not have a full talk schedule published by then, but we do hope to have published a long list of confirmed topics and presenters by then. Watch this space <https://gcc2021.sched.com/>. -- https://galaxyproject.org/

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rabbitmq erlang-crypto
by Luc Cornet 18 May '21

18 May '21

Dear all, I have a strange error with rabbitmq on ubuntu 20.04. The playbook was working previously on this OS but now I have this error: TASK [usegalaxy_eu.rabbitmq : install rabbitmq] **************************************************************************************************************************** task path: /home/galaxyluc/galaxy/roles/usegalaxy_eu.rabbitmq/tasks/Debian/install.yml:23 <galaxy.inbios.uliege.be> ESTABLISH LOCAL CONNECTION FOR USER: root <galaxy.inbios.uliege.be> EXEC /bin/sh -c 'echo ~root && sleep 0' <galaxy.inbios.uliege.be> EXEC /bin/sh -c '( umask 77 && mkdir -p "` echo /root/.ansible/tmp/ansible-tmp-1620999798.916904-12818219648644 `" && echo ansible-tmp-1620999798.916904-12818219648644="` echo /root/.ansible/tmp/ansible-tmp-1620999798.916904-12818219648644 `" ) && sleep 0' Using module file /usr/lib/python3/dist-packages/ansible/modules/packaging/os/apt.py <galaxy.inbios.uliege.be> PUT /root/.ansible/tmp/ansible-local-1239270zkwwo8m/tmpd5o4vaj2 TO /root/.ansible/tmp/ansible-tmp-1620999798.916904-12818219648644/AnsiballZ_apt.py <galaxy.inbios.uliege.be> EXEC /bin/sh -c 'chmod u+x /root/.ansible/tmp/ansible-tmp-1620999798.916904-12818219648644/ /root/.ansible/tmp/ansible-tmp-1620999798.916904-12818219648644/AnsiballZ_apt.py && sleep 0' <galaxy.inbios.uliege.be> EXEC /bin/sh -c '/usr/bin/python3 /root/.ansible/tmp/ansible-tmp-1620999798.916904-12818219648644/AnsiballZ_apt.py && sleep 0' <galaxy.inbios.uliege.be> EXEC /bin/sh -c 'rm -f -r /root/.ansible/tmp/ansible-tmp-1620999798.916904-12818219648644/ > /dev/null 2>&1 && sleep 0' fatal: [galaxy.inbios.uliege.be]: FAILED! => { "changed": false, "invocation": { "module_args": { "allow_unauthenticated": false, "autoclean": false, "autoremove": false, "cache_valid_time": 0, "deb": "/usr/src/rabbitmq-server-3.8.9-1.deb", "default_release": null, "dpkg_options": "force-confdef,force-confold", "force": false, "force_apt_get": false, "install_recommends": null, "only_upgrade": false, "package": null, "policy_rc_d": null, "purge": false, "state": "present", "update_cache": null, "upgrade": null } }, "msg": "Dependency is not satisfiable: erlang-crypto (< 1:24.0)|esl-erlang (< 1:24.0)\n" } Does anyone have any idea how to solve this ? Thanks, Luc ------------ Luc Cornet, PhD Bio-informatician Mycology and Aerobiology Sciensano

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cyverse-ansible.singularity
by Luc Cornet 10 May '21

10 May '21

Hello all, I have a problem with singularity while installing galaxy with ansible. ``` ASK [cyverse-ansible.singularity : Ubuntu package installation for v3.0 or newer] ************************************************************************* ok: [galaxy.inbios.uliege.be] TASK [cyverse-ansible.singularity : CentOS package installation for v3.0 or newer] ************************************************************************* skipping: [galaxy.inbios.uliege.be] TASK [cyverse-ansible.singularity : check if singularity binary exists] ************************************************************************************ ok: [galaxy.inbios.uliege.be] TASK [cyverse-ansible.singularity : Obtain current binary version] ***************************************************************************************** skipping: [galaxy.inbios.uliege.be] TASK [cyverse-ansible.singularity : download the singularity release] ************************************************************************************** fatal: [galaxy.inbios.uliege.be]: FAILED! => {"changed": false, "dest": "/tmp/singularity-3.7.0.tar.gz", "elapsed": 5, "msg": "Request failed", "response": "HTTP Error 404: Not Found", "status_code": 404, "url": "https://github.com/sylabs/singularity/releases/download/v3.7.0/singularity-…"} ``` The URL for singularity has changed, Do you know how can i fix that ? Maybe a more recent version of : ``` - src: cyverse-ansible.singularity version: 048c4f178077d05c1e67ae8d9893809aac9ab3b7 ``` Thanks for the help, Luc ------------ Luc Cornet, PhD Bio-informatician Mycology and Aerobiology Sciensano

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May 2021 Galaxy Newsletter: GCC2021 Deadlines Extended
by Dave Clements 04 May '21

04 May '21

Hello all, *The May 2021 edition of Galaxy News <https://galaxyproject.org/news/2021-05-galaxy-update/> is out! * The big news is that *several deadlines for the 2021 Galaxy Community Conference <https://galaxyproject.org/news/2021-05-galaxy-update/#community-news> have been extended, and the deadline for submitting James Taylor videos <https://galaxyproject.org/news/2021-05-galaxy-update/#featured-news> has been extended to this Friday.* And there are other upcoming deadlines too: - *ISMB/ECCB and BOSC 2021 abstracts <https://galaxyproject.org/news/2021-05-galaxy-update/#event-news> are due this Thursday.* - *Apply for the Galaxy Australia Variant Calling Workshops <https://galaxyproject.org/news/2021-05-galaxy-update/#event-news> by May 12.* We also have - *open positions <https://galaxyproject.org/news/2021-05-galaxy-update/#community-news>* - *webinars, CoFests, workshops, community meetups, and other events <https://galaxyproject.org/news/2021-05-galaxy-update/#event-news>*, - news about *public Galaxy platforms <https://galaxyproject.org/news/2021-05-galaxy-update/#galaxy-platforms-news>* , - recent *blog posts <https://galaxyproject.org/news/2021-05-galaxy-update/#galactic-blog-activity>* , - *training and doc updates <https://galaxyproject.org/news/2021-05-galaxy-update/#doc-hub-and-training-…>* , - recent *open-access Galaxy-related publications <https://galaxyproject.org/news/2021-05-galaxy-update/#publications>*, and - *new releases <https://galaxyproject.org/news/2021-05-galaxy-update/#releases>.* As always, thanks for using Galaxy, Dave Clements and Beatriz Serrano-Solano, Editors -- https://galaxyproject.org/

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galaxy-dev May 2021