November 2020 - galaxy-dev - lists.galaxyproject.org

Expose local filesystem to Galaxy?
by Sandra Maksimovic 15 Dec '20

15 Dec '20

Hi there, We are hosting an on-prem Galaxy instance in a HPC environment. Our research staff would like the ability to manipulate raw data that is located on the shared filesystem without having to manually upload it into Galaxy. Is this currently supported and would there be any related documentation? Thanks, Sandra

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Requesting a tool integration
by Muhammet A. Celik 21 Nov '20

21 Nov '20

To whom may it concern; We are writing to inquire on the possibility of contributing to the Galaxy pool of tools. At the outset, we thank the Galaxy community for all the hard work on the wonderful platform, which is of a big value to the scientific community. We are participants of the Open Life Science Project-2 (OLS-2) and are mentored by Dr. Mallory Freeberg, who is also CCed in this email. Our project is about creating a single pipeline integrating metagenomics tools for taxonomic classification. The pipeline would ease the work of those interested in metagenomic studies, especially those who do not have IT background or enough computational resources. We also want to include a visualization tool (Krona) to illustrate the output, since the standard output is typically a txt file. The selected tools for the taxonomic classification are Kraken2, Centrifuge and Clark, which are widely used and identified as the state of the art based on our literature review. Last week, we presented our work to Dr Berenice Batut (who is also CCed herein), who is an expert in the field. Thanks to her feedback and advice and that of Dr Mallory, we want to explore the prospect of porting our project onto the Galaxy platform, to benefit the wider community. We have checked both the Galaxy servers (https://usegalaxy.eu/ and https://usegalaxy.org) as well as the ToolShed to see if the tools that we want to deploy are already available on Galaxy. Kraken2 is available and is ready for use with various DB's. On the other hand, we were not able to find Centrifuge on the tools search section, although it appears in the ToolShed ( https://toolshed.g2.bx.psu.edu/view/jvolkening/centrifuge/be7bba8229c6) whereas Clark (http://clark.cs.ucr.edu/) is not available on the platform. Thus, we hope that you could import these tools on Galaxy so that we can port our pipeline(workflow) on the Galaxy platform. Thank you, Muhammet

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Galaxy Admin Training, Jan 25-29, online. global, and free.
by Dave Clements 18 Nov '20

18 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/

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Release of Galaxy 20.09
by Marius van den Beek 17 Nov '20

17 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!

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Subscription
by Muhammet A. Celik 17 Nov '20

17 Nov '20

a.muhammetcelik(a)gmail.com

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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/

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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/

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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.

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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/

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