galaxy-dev

galaxy-dev@lists.galaxyproject.org

10006 discussions

Galaxy Admin Training, Jan 25-29, online. global, and free.
by Dave Clements 19 Nov '20

19 Nov '20

Hello all, We are now accepting applications for the January 2021 Galaxy Admin training workshop. This will be offered online and around the world, and will be free: https://galaxyproject.org/events/2021-01-admin-training/ If you administer or plan to administer a Galaxy instance then please consider applying for this workshop. Space is limited, and we expect applications to be competitive. The application deadline is December 18. Thanks, Dave C on behalf of the workshop instructors. -- https://galaxyproject.org/

1 0

Release of Galaxy 20.09
by Marius van den Beek 18 Nov '20

18 Nov '20

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 20.09. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/20.09_announce.html and user facing release notes are at https://docs.galaxyproject.org/en/master/releases/20.09_announce_user.html. A few release highlights are: GTN In Galaxy -------------------- The Galaxy Training Network tutorials can now be accessed from within Galaxy using the graduation cap icon. For updated tutorials, tools will be highlighted as blue buttons. When clicked, these buttons will hide the GTN and take you directly to the correct version of the correct tool within the Galaxy interface. Plugin framework for uploading datasets ------------------------------------------------------ Galaxy administrators can now configure different sources from which users may upload files. These include global or user-specifc webdav servers, dropbox accounts as well as FTP and regular filesystem locations. Developers can add new types of sources by adding PyFileSystem2 <https://docs.pyfilesystem.org/en/latest/introduction.html> compatible plugins. Upload directly from the Tool Form ---------------------------------------------- Datasets can now be uploaded directly from the Tool Form. Workflow import from GA4GH TRS servers --------------------------------------------------------- Galaxy can now search and import workflows from GA4GH TRS servers, such as Dockstore <https://dockstore.org/> and WorkflowHub <https://workflowhub.eu/>. We hope that sharing workflows on these platforms will facilitate re-use and collaboration. Simplified workflow submission form ------------------------------------------------ Galaxy now presents a simpler and cleaner interface for submitting workflows that focuses on the parameters to set and datasets to choose. Accelerated batch job creation and workflow step scheduling --------------------------------------------------------------------------------- Galaxy now batches database interactions for the creation of batch jobs. For large batches of jobs this can speed up job creation by 100-fold or more. Check out the release notes 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!

1 0

Subscription
by Muhammet A. Celik 17 Nov '20

17 Nov '20

a.muhammetcelik(a)gmail.com

1 0

Galaxy Developer Round Table: Working with the GTN, TODAY
by Dave Clements 12 Nov '20

12 Nov '20

Hi All, The next Galaxy Developer Round Table STARTS IN 30 MINUTES, at Noon US Eastern. It will be a discussion about working with the Galaxy Training Network. Links are here: https://galaxyproject.org/events/2020-11-12-dev-roundtable/ Hope to see you there, Dave C -- https://galaxyproject.org/

1 0

November 2020 Paper Cuts Day: Nov 18
by Dave Clements 11 Nov '20

11 Nov '20

Hello all, The second Galaxy Paper Cuts day will be held on Wednesday November 18. It will be a day long, around-the-world event, with calls about every 3 hours, plus Gitter chat and support all day. https://galaxyproject.org/events/2020-11-papercuts/ "Paper cuts" are annoying, but relatively easy to fix bugs. They are also a great way to become familiar with how to contribute code and other updates. This paper cut event applies to the entire Galaxy ecosystem. In addition to learning and fixing, you can also help by 1) Creating GitHub issues for anything in Galaxy that bugs you and is likely to be easy to fix.* 2) Advertising this event in your communities. We are particularly reaching to research software engineers and students. We hope to see you online next week! Cheers, Dave C on behalf of the PaperCuts organizers * What's easy to fix? Trust your instincts on this. We would like to hear about glitches, even if they turn out to be harder to fix. -- https://galaxyproject.org/

1 0

pbs_python + python 3 issue
by Sandra Maksimovic 09 Nov '20

09 Nov '20

Hi, Has anyone out there had any success installing the pbs_python module into a Python 3+ Galaxy installation? I run into the following issue when installing https://github.com/ehiggs/pbs-python as per the documentation. # python setup.py install File "setup.py", line 68 print "Version: %s is not supported" %(PBS_VERSION) ^ SyntaxError: invalid syntax I provide the PBS/Torque version via the PBS_PYTHON_INCLUDE_DIR environment variable but it doesn't seem to detect the version properly. 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.

2 1

November 2020 Galaxy News
by Dave Clements 03 Nov '20

03 Nov '20

Hello all, The November newsletter is out: https://galaxyproject.org/news/2020-11-galaxy-update/ Topics: * JXTX: The James P. Taylor Foundation for Open Science New name, and meet our first awardees * Event news Lots of them, with one starting today (if you are in Australia / East Asia) Galaxy Admin Training will be in late January * Galaxy platform news GalaxyTrakr, Galaxy Africa, Australia, Europe, and UseGalaxy.* * Blog post Advanced Microbiology with Galaxy and TIaaS at Strathclyde * Training material and doc updates Metaproteomics, calling variants, and auto-generated video (!) * Publications Pub curation is on hiatus, but some pubs just can't be ignored :-) * Open positions At 8 organizations. (Yes eight!) * New releases The new Galaxy Language Server Thanks for using Galaxy, Dave C and Beatriz -- https://galaxyproject.org/

1 0

Galaxy Developer Round Table: Tool testing and deployment, Oct 29
by Dave Clements 29 Oct '20

29 Oct '20

Hi All, The next Galaxy Developer Round Table will be Thursday, October 29, at Noon US Eastern. It will be a roundtable discussion on tool testing and tool deployment issues. Links (including time zone conversion) are here: https://galaxyproject.org/events/2020-10-29-dev-roundtable/ Hope to see you there, Dave C (channelling actual developers!) -- https://galaxyproject.org/

1 0

Galaxy Paper Cuts Day: Wednesday October 19
by Dave Clements 20 Oct '20

20 Oct '20

Hi all, We are organising the Galaxy Paper Cuts contribution fest this Wednesday*: https://galaxyproject.org/events/2020-10-papercuts/ Paper Cuts are small irritants that introduce friction when using or administering Galaxy. We want to 1) get rid of them, thus improving Galaxy 2) grow the contributor community! Want to help / learn / join? Please sign up. (You can also just show up, but then you won't get a reminder email.) Between now and the end of Wednesday, there are a couple of big ways you can help: 1. Participate! 2. Create GitHub issues for things that you find irritating, in any part of the Galaxy ecosystem 3. If you manage a Galaxy component (e.g., BioBlend, Planemo, ...) create a tag for paper cuts, tag any appropriate issues with it, and then let us know what tag you used.** Hope to see you on Wednesday, Dave C channeling Simon, Björn, and Dannon (in time zone order!) * This Wednesday == 21 hours from now in Australia ** Or just update the paper cuts page in the hub directly. -- https://galaxyproject.org/

1 0

Segmentation fault
by James White 10 Oct '20

10 Oct '20

We have installed Galaxy on a local server with these os and programs: CentOS Linux release 8.1.1911 galaxy release_20.09 Python 3.6.8 When we configured object store for disk store it worked fine. We tried to configure Google Compute Platform and followed the instructions to create a bucket and install the .json key. When we test it it starts for a short time and then fails. /lib64/libpython3.6m.so.1.0(+0x1cd274) [0x7f1f5d9da274] /lib64/libpthread.so.0(+0x82de) [0x7f1f5d5f52de] /lib64/libc.so.6(clone+0x43) [0x7f1f5cb9ce83] *** end of backtrace *** run.sh: line 91: 18100 Segmentation fault (core dumped) .venv/bin/uwsgi --yaml /usr/local/galaxy/config/galaxy.yml --static-safe /usr/local/galaxy/client/src/assets Will appreciate any suggestions. Jim W -- Programmer Dept. of Entomology and Plant Pathology N.C. State Univ. Raleigh, N.C.

1 0

← Newer
1
...
4
5
6
7
8
9
10
...
1001
Older →

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

galaxy-dev