galaxy-dev

galaxy-dev@lists.galaxyproject.org

10006 discussions

January 2021 Galaxy Newsletter
by Dave Clements 07 Jan '21

07 Jan '21

Hello all, We are pleased to announce the first newsletter of 2021. As you can see there is a lot happening this month, starting with a working groups call about one hour from now. Thank you for persevering through 2020, and we hope that 2021 will be a better year for the world, and for this community. Dave Clements and Beatriz Serrano-Solano - *Event news <https://galaxyproject.org/news/2021-01-galaxy-update/#event-news>*: - 2nd Galaxy-ELIXIR webinar series, *starts January 20* - Galaxy Developer Roundtables, *January 7 & 21* - Papercuts CollaborationFest: *January 21* - Future Galaxy Admin Trainings, *Register your interest* - Tripal CodeFest 2021: *January 11-15* - Structural Variant Detection using ONT Data, *January 26* - GTN Smörgåsbord: A Global Galaxy Course. *Register by February 1* - Single-cell RNA-seq & network analysis using Galaxy and Cytoscape, *Apply by 26 February* - *Galaxy platform news <https://galaxyproject.org/news/2021-01-galaxy-update/#galaxy-platforms-news>:* - UseGalaxy.no - VINYL on Laniakea - W4M on UseGalaxy.fr - Center for Phage Technology server upgraded and improved - Plus more UseGalaxy.* news - *Blog posts <https://galaxyproject.org/news/2021-01-galaxy-update/#galactic-blog-activity>:* - Involvement of the Galaxy community in OLS-2 and invitation to apply to the next cohort - DDA and DIA proteomic analysis in Galaxy - GTN plant-related trainings - *Training material and doc updates <https://galaxyproject.org/news/2021-01-galaxy-update/#doc-hub-and-training-…>*: - Videos: Galactic Introductions - Videos: Quick Tips - *Publications <https://galaxyproject.org/news/2021-01-galaxy-update/#publications>* - Metaproteomics, CorGAT (SARS-CoV-2), GAIT-GM (metabolites), and training - *Q: Who's hiring? <https://galaxyproject.org/news/2021-01-galaxy-update/#whos-hiring>* - Europe: - Norwegian University of Life Science, IFB, VIB - North America: - Roche, Johns Hopkins (AnVIL, 2 positions; Galaxy, 2 Positions) - *New releases <https://galaxyproject.org/news/2021-01-galaxy-update/#releases>*: - Planemo 0.74.1 -- https://galaxyproject.org/

1 0

Expose local filesystem to Galaxy?
by Sandra Maksimovic 16 Dec '20

16 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

2 2

Galaxy Papercuts CoFest Day: December 17
by Dave Clements 14 Dec '20

14 Dec '20

Hello all, The third Galaxy Paper Cuts day will be held on Thursday, December 17. It will be a day long, around-the-world event, with calls about every 3 hours, plus Gitter chat and support all day. See https://galaxyproject.org/events/2020-12-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 * Creating GitHub issues for anything in Galaxy that bugs you and is likely to be easy to fix.* * Advertising this event in your communities. We are particularly reaching to research software engineers and students. We hope to see you online on Thursday! Cheers, Dave C on behalf of the PaperCuts organizers * What’s easy to fix? Trust your instincts on this. We want to hear about glitches, even if they turn out to be harder to fix. -- https://galaxyproject.org/

1 0

December 2020 Galaxy Newsletter: And what a month it is
by Dave Clements 08 Dec '20

08 Dec '20

Hello all, The December 2020 newsletter is out https://galaxyproject.org/news/2020-12-galaxy-update/ And there is a lot to it: ---------------- Event news: Webinars: Use Galaxy anywhere, right now, December 9 Chloroplast Genome Assembly, December 10 First Metabolomics Community Call, December 10 Galaxy Developer Round Table: Working Groups, December 10 Papercuts CollaborationFest: December 17 Galaxy Admin Training: Apply by December 18 Tripal CodeFest 2021: January 11-15 GTN Smörgåsbord: A Global Galaxy Course. Register by February 1 Galaxy platform news: CLIP-Explorer, a new server for CLIP-Seq data GenAP expansion funded by CANARIE (Canada!) UseGalaxy.eu gets more storage and GPUs through deNBI-Cloud Plus more UseGalaxy.* news Blog posts: Outcome of the BioHackathon Europe Accessible single-cell RNA-sequencing bioinformatics training using Galaxy TIaaS and training feedback Training material and doc updates: Chloroplast genome assembly Compute and analyze Essential Biodiversity Variables with PAMPA toolsuite 16S Microbial analysis with Nanopore data Publications Metaproteomics, CLIP-Explorer, GIANT, and package management is your friend Q: Who's hiring? Europe: Max Planck IIE, University of Oslo, Hannover Medical School, EMBL Rome, Norwegian University of Life Science, Sorbonne-Université North America: Roche, Johns Hopkins (AnVIL, 2 positions; Galaxy, 2 Positions), Cleveland Clinic A: Everyone, it seems. New releases: Galaxy 20.09 ENA submission OMERO accessible from Galaxy CloudLaunch Other news too -------------------- Happy Holidays! Dave C and Beatriz, on behalf of, well, everyone -- https://galaxyproject.org/

1 0

***UNCHECKED*** Get Expert Plumbing Services Round The Clock From Certified Plumbers!
by turstedcaptain＠gmail.com 05 Dec '20

05 Dec '20

Plumbing issues are very common as they didn’t come with any prior notices. From clogged drains to leaky faucets we need to tackle various common and complex issues which need to be resolved on time. If you are one of those whose life is affected by unwanted plumbing issues then search for the Plumbers Near Me or reach out to us on our toll-free number for reliable plumbing services. Plumbers available at our platform are highly skilled, professional and experienced. They also help you in strategizing and maintaining plumbing systems or your commercial or under construction sites. Expert Plumbing Services which makes us unique: • Same day plumbing inspections. • Drug tested & verified plumbers. • Round the clock availability and services. • Flat rates. • Prior generated bills for a hassle-free experience. • No hidden charges https://www.trustedcaptain.com/plumbing-services-near-me.html

1 0

Get Expert Plumbing Services Round The Clock From Certified Plumbers!
by turstedcaptain＠gmail.com 05 Dec '20

05 Dec '20

1 0

Get Expert Plumbing Services Round The Clock From Certified Plumbers!
by turstedcaptain＠gmail.com 05 Dec '20

05 Dec '20

1 0

hvac replacement near me
by saransh＠swasthyakart.com 04 Dec '20

04 Dec '20

https://www.trustedcaptain.com/hvac-repair-services-near-me.html When you search for the HVAC Service Provider Near Me you can easily connect with Our licensed HVAC specialists who have years of experience in fulfilling residential and commercial needs with unmatchable Heating & Air Conditioning services. Our technician delivers pleasant HVAC services on a single call for HVAC Installation, Repair or maintenance services. It is very crucial to get linked with the specialists who can provide both unmatchable & budget-oriented quotations when it comes to Heating & Air Conditioning services. Our technicians use the most superior equipment and strategies which make them more trusted & professional.

1 0

Two Important Galaxy Calls Next Week
by Dave Clements 03 Dec '20

03 Dec '20

Hi All, There are two important Galaxy related calls next week. Please consider: * spreading the word about the first one to your communities. * attending both Details are below. Thanks, Dave C ============= Please consider attending this one, and announcing it to your communities: **Use Galaxy on the web, the cloud, and your laptop too: Options for using Galaxy: everywhere and right now** Wednesday, December 3rd, 11am Eastern US time (see your time: https://bit.ly/2VABo3X) https://galaxyproject.org/events/2020-12-webinar-where/ This Galaxy webinar will introduce the many options for using Galaxy right now and anywhere in the world. We'll cover * Publicly accessible Galaxy servers on the web (there are over 100 of them) * Research and commercial cloud platforms, from Australia (Nectar) to the US (Jetstream, AnVIL), and everywhere in between (CloudLaunch) * On your laptop, using pre-packaged containers and virtual machines. The webinar will be at 11am Eastern US time (see your time). Enis Afgan, Anton Nekrutenko, and Mike Schatz will present. Interested? Please sign up now: https://bit.ly/2020-12-webinar-register ============ Please consider attending this one: **Get Involved with Galaxy: Introducing Galaxy Working Groups** Thursday, December 10, Noon Eastern US (see your time: https://bit.ly/3g6J8nN) https://galaxyproject.org/events/2020-12-10-dev-roundtable/ Galaxy has grown a lot of the years, going from a project at one university in 2005 to the global community it is today. Several parts of the Galaxy ecosystem have become avowedly and obviously community driven during that time, including tools, code, training, and several other international efforts. It is past time to push this global model to other areas of Galaxy as well. At the December 10 Galaxy Developer Roundtable we will introduce Galaxy Working Groups as a means for the community to help manage and contribute to key parts of the Galaxy ecosystem. If you are interested and are potentially willing to contribute some of your time and effort to helping the global Galaxy effort, then please attend this roundtable on December 10. If you can't make it, the gathering will be recorded and published shortly after the event. -- https://galaxyproject.org/

1 1

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

2 2

← Newer
1
2
3
4
5
6
7
8
9
...
1001
Older →

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

galaxy-dev