Galaxy training contribution fest - 6-7th October

[bgruening]

Dear training enthusiast,

The Galaxy Training Network (GTN) is planning a contribution fest to consolidate our training material and improve the overall training experience in Galaxy on the 6.-7th October 2016!

More information about this project can be found here: https://gist.github.com/bgruening/a54a8600c5cddca82424ad13569708c3

and a small presentation is here: http://bgruening.github.io/training-material/shared/slides/project_presentation#/

This will be an online contribution fest and the fun to contribute should be priority one! There is enough to work on in all areas, from programming to fix spelling mistakes. So everyone is welcome to improve the Galaxy training material.

Organisation

We will coordinate ourselves over Gitter: https://gitter.im/Galaxy-Training-Network/Lobby In addition we will be available at this hangout https://hangouts.google.com/call/bapluwa3s5deveo5flrcwqzqpme A list of this that can be worked on during the contribution fest can be found here: https://github.com/bgruening/training-material/issues

How to start contributing?

A small checklist to help you with this contribution fest

• Create a GitHub account
• Check the CONTRIBUTING.md
• Become familiar with this repository structure
• Connect to the Gitter chat with your GitHub account and say hello :)
• Check out the issues and PR
• Add you on the CONTRIBUTORS.md
• Add you on the Galaxy map
• Register for the hacktoberfest
• (If you like) Assign yourself as a maintainer of a topic and take over responsibilities
• Assign yourself to an issue or a PR when you find one (or create one) and tell it on Gitter
• Ask if you have any question

Ciao, Bérénice and Bjoern

[jmchilton]

Cool beans - I'll try to work on https://github.com/galaxyproject/galaxy/pull/2283 during this. I don't know how that would fit into your master plan but it is Markdown and HTML slides and important documentation - but it is not reveal.js though. The good part of the approach though is that it seems to fit into Sphinx well. Maybe we should harmonize approaches.

[friedue]

sounds great! anybody in the New York City area who'd like to meet up for this?

[bgruening]

@jmchilton sounds good. Currently we agreed upon reveal.js here: https://github.com/bgruening/training-material/issues/8 But I think as everythin is markdown we can inter convert everything.

@friedue great you can join!

Anyone nearby Freiburg/Germany wants to join? Afaik @hrhotz will visit us on 6th to work with us in Freiburg and others are welcome too!

[bgruening]

@vipints you are still in New York, aren't you? :)

[vipints]

Björn, Yeah I am still here in NYC :) Planning to join for the event virtually.

[vipints]

@friedue: I am in MSKCC

[bgruening]

@friedue I kindly introduce you to @vipints! He knows TÜ! @vipints I kindly introduce you to @friedue! She was in FR! ;)

[stevekm]

I this training material for using Galaxy, or setting up Galaxy?

[bgruening]

@stevekm both. We have collected material for admins: https://github.com/bgruening/training-material/tree/master/Admin-Corner, Users and Developers.

[stevekm]

Is there a formal step-by-step guide for Admins getting started with Docker and setting it up as a service? I looked through the items there, and have gone through the documentation in other places but so far haven't found a complete walk-through; had plans to write one myself once I figure it all out. Also, I had issues with the link in the readme on that page, might need to change it to this? http://galaxy.slides.com/bgruening/the-galaxy-docker-project#/

[bgruening]

@stevekm the link is working for me :( What do you see. We have a lot of documentation about the Docker project here: https://github.com/bgruening/docker-galaxy-stable I hope this helps.

[stevekm]

@bgruening I think the live part of the URL is trying to start a live session; for me it just hangs on the first slide trying to establish a connection to your account. The URL I listed shows the slides only. The Docker doc's have been very useful but I've still had to pull together info from many other sources (e.g. Ansible playbooks) to get things configured; doc's for the other aspects weren't written in the context of using Docker so its been a little extra confusing to figure out how to piece everything together.

[bgruening]

@stevekm are you using this Container or developing for it/with it? The latter is indeed not covered. Happy to accept patches.

[stevekm]

Right now I am trying to get the Galaxy Docker set up as a service at my institution.

[slegras]

Hi! that's a pretty nice initiative! Have you spit up the 2 days into topics; I'd like to join but I can't join the two entire days.

[bgruening]

@slegras great to see you here! we haven't any topics, I thought everyone works on a specific training or that small groups working on a specific training over the two days. But I'm open for suggestions. @stevekm let ma know if you get stuck and how we can improve our documentation.

[slegras]

Ok, I'll be there (on the 6th) and see to which topic(s) I can contribute :). Prior to the Hackathon could we list the topics we could address ?

[stevekm]

how does an 'online contribution fest' work? Is there a website or physical location where people are meeting?

[bgruening]

We will be on gitter/IRC as you like I will open an hangout and will start with a short presentation and what we are aiming for in this project. Then everyone can start gathering together in groups, get things done, ask questions, create PR, have fun to work together :)

[lecorguille]

As I already said, I'm in to contribute on the dev-corner

[hrhotz]

unfortunately, I won't be able to join in person in Freiburg on Thursday, but will try to do some work in the admin corner on Thursday/Friday

[shiltemann]

I will join the hackathon as well. We have some training materials here: https://github.com/ErasmusMC-Bioinformatics/galaxy-courses, some of which we could maybe adapt/integrate here. And I can help out with the introduction, NGS, and RNA-seq topics in general as we teach those a lot ourselves too. And I could help out in dev-corner for tools/IEs/viz as well.

I would also like to see a metagenomics topic, I've started working on a galaxy training (following this repos' style) for the Mothur MiSeq SOP (http://www.mothur.org/wiki/MiSeq_SOP) with some additional visualisation steps (krona/phinch etc) ..and in the long term would like to add a training for qiime as well (but will need to work on the tools themselves first).

[bgruening]

@hrhotz too bad! I ordered already cookies ;) @shiltemann sounds wonderful! I have updated the description above and added a organisation section.

[devengineson]

Hi @bebatut @bgruening and all Galaxy lovers, EnginesOn, @jennydg @fjrmoreews @yvanlebras, are insterested to participate to this new hackathon time! The objectives can be for us to improve the training tutorial for RAD-Seq and for Multi-QC developped by @yvanlebras and @cmonjeau. This will also be the opportunity for Jennifer, future leader of the company, to get involved in the community and get familiar with this type of event..... @bgruening is your cookies sendable by ftp ;) ?

[bgruening]

@devengineson what can I say? Engine On! Let's rock the Galaxy training world!

[jennydg]

Hi @bebatut @bgruening! @devengineson will be represented by myself, with help from @yvanlebras, @fjrmorreews, @cmonjeau but I will probably not be able to cover the whole 2 days. I already know I won't be available tomorrow morning.

[bgruening]

@jennaj sure thing! The aim is to have fun and work with friends don't feel bad if you can not join :)

[yvanlebras]

@bgruening I think there is a Jenni mistake ;) in your last message between @jennaj and @jennydg

I like your hfawwf (have fun and work with friends) concept !

[bgruening]

Upps, you are right! @jennydg my bad sorry. hfawwf!

[gmauro]

Hi all, I will try to join the hackathon both days with.

[bgruening]

@gmauro great! See you tomorrow!

[mwolfien]

Hey, I will join both days as well! Can't wait for tomorrow =)

[tnabtaf]

I'll join tomorrow and Friday. I'm Pacific US time, so will be on the tail end of both days.

[stevekm]

are there details up yet about how/when to join?

[bgruening]

@stevekm please read the issue description at the top. I have tried to collect all information's there. Moreover, there is no when. People from all over the world will join and depending on the timezone this can vary a lot. Just join us on gitter and assign yourself to one of the https://github.com/bgruening/training-material/issues or contribute your own training material! HFAWWF - (have fun and work with friends) :)

[stevekm]

also @friedue @vipints I am in NYC too let me know if there's a meetup for this

[jennaj]

I posted this to Biostars in hopes of attracting some sci users. Hope Ok! https://biostar.usegalaxy.org/p/19971/

I'll also be joining during both days when I can. See you all there

[bgruening]

@jennaj more than ok! Fantastic! Thanks!

[bgruening]

Ok Europe we will start the contribution fest! :)

[friedue]

@stevekm Vipin and I will join tomorrow, I've booked a room at Weill Cornell for this (send me an email to frd2007 at med.cornell.edu to get the exact location, would be great to have you around, too!)

[bgruening]

Hi all,

I'm so sorry we wanted to publish a nice writeup about this great event, but we are swamped with preparation for the Swiss/German Galaxy workshop here in Freiburg. I promise to get to this as soon as possible.... Many thanks to you all again! This was a great event and we hope to organize a similar event soon.

[yvanlebras]

Thank you Björn and Bérénice for the amazing work to help us contribute in the best way!!!!!

I look forward to have time to finish a first complete version of the Stacks training material!!!!

Tscüss,

Yvan

----- Mail original -----

De: "Björn Grüning" notifications@github.com À: "bgruening/training-material" training-material@noreply.github.com Cc: "Yvan Le Bras" yvan.le_bras@irisa.fr, "Mention" mention@noreply.github.com Envoyé: Mardi 18 Octobre 2016 14:25:37 Objet: Re: [bgruening/training-material] Galaxy training contribution fest - 6-7th October (#58)

Hi all,

I'm so sorry we wanted to publish a nice writeup about this great event, but we are swamped with preparation for the Swiss/German Galaxy workshop here in Freiburg. I promise to get to this as soon as possible.... Many thanks to you all again! This was a great event and we hope to organize a similar event soon.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub , or mute the thread .

---

Yvan Le Bras, PhD @Yvan2935 <°))))>< e-Biogenouest project http://www.e-biogenouest.org CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042 Rennes Cedex tél.: +33 (0) 2 99 84 71 79 / +33 (0) 6.10.43.96.51 yvan.le_bras@irisa.fr

[bgruening]

A little bit late but here is our summary!!!

https://docs.google.com/document/d/1pThnwvQKvdN1C0ub1QWoXcWp71QinZb_msUKHLFxfFI/pub

Thanks again!

[hrhotz]

very nice text! a big Thank you to @bebatut and @bgruening