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Bioinformatics for the masses? (link above) nice bit by David Weiss
David Weiss
@davidweisss
Thanks for the thumbs up Stephen!
I did a pr proposing to add a reference to a recent survey highlighting problems bioinformaticians are facing, with some insights into informatics-pipelines-related problems: http://figshare.com/articles/Bioinformatics_infrastructure_and_training_summary/1572287
Stephen J Newhouse
@snewhouse
@davidweisss no probs! looking forward to meeting (everyone) tomorrow. Thanks for the link! Interesting reading....
Amos Folarin
@afolarin
Amos Folarin
@afolarin
Great to see you all! Will be in touch with plans to keep the ball rolling
Stephen J Newhouse
@snewhouse
absolute pleasure meeting you all! Amos and I will be in touch soon
Paolo Di Tommaso
@pditommaso
thank you guys for organising such a nice event
looking forward to hearing from you soon.
Stephen J Newhouse
@snewhouse
@davidweisss sorry we didnt get to chat more! Thanks for the coverage! You and @chapmanb have some great conference notes! We'll be in touch also.
@chapmanb I am excited about putting the best of bcbio-nextgen + NGSeasy together and starting the mother of all NGS Tools sets with you! "NGS for the Masses".
docker + flocker + weave + kubernetes + nextflow + MPS + cwl == fun times ahead...(I hope)
@pditommaso thanks for helping make it a great 2 days!
Brad Chapman
@chapmanb
Steve and Amos -- awesome, thanks so much for everything. Looking forward to working closer together. I'll be actively working to make bcbio more friendly for combining and contributing.
Amos Folarin
@afolarin
It was unfortunate we couldn't get Arvados to talk but if anyone hasn't see their video (10mins) it is really relevant http://curoverse.com/demo
Stephen J Newhouse
@snewhouse
@chapmanb looking forward to working with you! will be on contact soon to get the ball rolling on scoping out NGS dev with you all
Brad Chapman
@chapmanb
Brilliant. Practically I'm working on transitioning to CWL which should provide increased documentation and interoperability of bcbio components; I hope that will help with getting started. Tons to work on so happy to collaborate however works best.
Stephen J Newhouse
@snewhouse
@pditommaso got any tips before I start deving up a nextflow pipeline for some of our NGS work? am about to start trawling through all of your .nf files on git. fun and games ahead :smile:
Paolo Di Tommaso
@pditommaso
Hi
Stephen J Newhouse
@snewhouse
@pditommaso hello
Paolo Di Tommaso
@pditommaso
and do not use absolute paths in your process scripts
yes, try to think process as self-conatined tasks
yes, try to think process as self-contained tasks
(I'm at the dockercon and there's a very bad connection ..)
Stephen J Newhouse
@snewhouse
@pditommaso no worries..thanks for the tips. Conference centers need to sort their wifi out ;)
Paolo Di Tommaso
@pditommaso
well, to many people using the wi-fi!
anyway for any other doubts do not hesitate to message me
Stephen J Newhouse
@snewhouse
Cheers. Will do!
Amos Folarin
@afolarin
slides up on F1000 Channel. just missing a few http://f1000research.com/channels/containers?&selectedDomain=SLIDES
Paolo Di Tommaso
@pditommaso
nice work guys
Stephen J Newhouse
@snewhouse
Hi All, I will be creating a project on https://www.overleaf.com soon to start drafting a position paper/editorial covering Bio in Docker & Container Virtualization in Bioinformatics for the F1000 Channel of the same name :) http://f1000research.com/channels/containers. We will be inviting all of you to conrtibute. Please do! To Cover a lot of the stuff we all presented and discussed at the conference: problems in bioinformatics, dependencies, reproducibility, vms/docker, cwl, nextflow, MPS+NextflowWorkbench, education of biologists and making things easy, our solutions and recommendations ie every new tool published should include a Dockerfile ( & list of dependencies & build and test env?) etc etc….lets also start our own “Awesome List of Bio in Docker Tools”
Brad Chapman
@chapmanb
Steve, great work getting this together. Thank you. Regarding listing docker tools, @briandoconnor and team have an awesome new initiative called Dockstore that collects containers along with CWL descriptions of use: https://www.dockstore.org/
Stephen J Newhouse
@snewhouse
Brad, this is great. Cheers. @briandoconnor we’ll be in contact soon
Amos Folarin
@afolarin
@snewhouse just brought this to my attention. A potential point of distribution for dockerized tools (using GA4GH and CWL) https://www.dockstore.org/
Brian O'Connor
@briandoconnor
hi folks!
Stephen J Newhouse
@snewhouse
@briandoconnor howdy!
Brian O'Connor
@briandoconnor
We’ve put up a survey on how to prioritize development for Dockstore.org in the future: http://goo.gl/forms/WCq7eVhOAv It would be great to get folk’s feedback on this.
Stephen J Newhouse
@snewhouse
@briandoconnor nice. form filled!
Brian O'Connor
@briandoconnor
Great, thanks much @snewhouse
Amos Folarin
@afolarin
@briandoconnor filled. Might be nice to be able to tie into projects like Portus https://github.com/SUSE/Portus for hosting private docker images (this might have the same attraction for users/organisations that want to manage their own private work, in the same way that GitLab is used)
Stephen J Newhouse
@snewhouse
Happy New Year All!
Paolo Di Tommaso
@pditommaso
Hope you have enjoyed you holidays!
Paolo Di Tommaso
@pditommaso
Something to keep an eye on
Amos Folarin
@afolarin
Yeah, saw that yesterday.. I had a chat sometime back with the two Matts from Jetstack and it sounded like this was a direction Docker might be travelling
Paolo Di Tommaso
@pditommaso
You may be interested
Björn Grüning
@bgruening
Please spread the news: bioconda/bioconda-recipes#2297