December 2018 - galaxy-dev - lists.galaxyproject.org

Please nominate training topics for GCC2019 by Dec 31
by Dave Clements 05 Dec '18

05 Dec '18

Hi All, The *2019 Galaxy Community Conference (GCC2019)* <https://galaxyproject.org/events/gcc2019/> will be held in be held in *Freiburg, Germany, 1-6 July*. Like previous Galaxy Community Conferences <https://galaxyproject.org/gcc/>, GCC2019 will feature invited keynotes, accepted talks, posters, demos, birds-of-a-feather gatherings and *training*. The format of GCC2019 will be a bit different than the previous years: it starts with 1 day of training and then 3 days with more specialized training sessions aligned with talks. *You can read more about the new format on the conference FAQ <https://galaxyproject.org/events/gcc2019/faq/#what-will-be-the-format-for-g…>.* *The training topics that are offered are determined by the community so BY YOU! <https://docs.google.com/forms/d/1fBPjEmw7Td52rhBnC0SvflnQCD7Ue5IMJ9RkM0SjnY…>* Please give some thought to what topics you would like to see offered, or that you would like to offer, and then submit them as topic nominations <https://docs.google.com/forms/d/1fBPjEmw7Td52rhBnC0SvflnQCD7Ue5IMJ9RkM0SjnY…> . Nominated topics can cover a wide range. For example: - Introduction to Using Galaxy - Scientific topic oriented trainings - Community specific trainings - Development and administration around Galaxy - Train the trainers This list only shows some examples. *Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic.* If you are looking for ideas, see the topic nominated in: 2016 <https://galaxyproject.org/news/2018-12-galaxy-update/bit.ly/gcc2016noms>, 2015 <https://galaxyproject.org/news/2018-12-galaxy-update/bit.ly/gcc2015vote>, 2014 <https://galaxyproject.org/news/2018-12-galaxy-update/bit.ly/1s6NtMN>, 2013 <https://galaxyproject.org/news/2018-12-galaxy-update/bit.ly/1i2j1gN> and the Galaxy Events page <https://galaxyproject.org/news/2018-12-galaxy-update/galaxyproject.org/even…> . Training nomination is open from *December, 1st* to *December, 31*. Topics will be compiled into a uniform list by the GCC2019 Organizing Committee, and topics will be voted on by the Galaxy Community from *January, 15th* to *January, 31st*. -- https://galaxyproject.org/ https://usegalaxy.org/

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December Galactic News
by Dave Clements 03 Dec '18

03 Dec '18

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XMLs not reloading in all processes (UWSGI)?
by D K 03 Dec '18

03 Dec '18

I'm running version 18.05 and have noticed that when updating the tool_conf.xml that changes don't always get loaded in all processes (e.g. if I hit reload sometimes my changes show up and sometimes they do not). Also, if I try to run a new tool I've added sometimes this will fail presumably because that process doesn't have the update. The only fix for this seems to be a galaxy restart. I've turned watchdog on and am using the UWSGI + mules strategy. Any suggestions?

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Fastq.gz datatype not recognized on import to data library
by Previti 03 Dec '18

03 Dec '18

Dear all, In my ongoing saga concerning our data libraries, I came across another issue after our update from 17.09 to 18.05. When trying to import fastq.gz files into a data library (linking the files from a user directory), the format is not recognized automatically. I specifically have to set the data type to fastq.gz in order for it to work at all and even then it sometimes ends up throwing an error (state = error). Is there anything in particular I need to change to make this work reliably? Cheers, Christopher -- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661 christopher.previti(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist. Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung. Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.

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