These are chat archives for chapmanb/obf-codefest

21st
Jul 2017
Hilmar Lapp
@hlapp
Jul 21 2017 01:37
Looks like I'm finally flying to Prague. Too bad I've had to miss today.
Brad Chapman
@chapmanb
Jul 21 2017 04:44
Have a safe flight Hilmar, sorry about all the delays and looking forward to seeing you when you make it in.
Heather L. Wiencko
@HLWiencko
Jul 21 2017 06:59
Morning everyone. Duty calls and I have some stuff to take care of this morning. Not sure if I'll make it today, if I do it'll be later in the afternoon, if not I'll see you all at BOSC. :)
Brad Chapman
@chapmanb
Jul 21 2017 07:00
Thanks Heather, hopefully see you later tonight.
We're just getting started here this morning, will plan on doing morning organization in a half hour.
There is a new hangout for anyone who wants to joint remotely: https://hangouts.google.com/call/46cq2fdgbvhmjds4nybn4tipiay
We also need to prepare slides for Codefest presentation at BOSC and slides are started and linked from: https://www.open-bio.org/wiki/Codefest_2017#Logistics
Brad Chapman
@chapmanb
Jul 21 2017 08:02
Morning updates in 2 minutes if anyone remote wants to listen in.
(two links there)
Paolo Di Tommaso
@pditommaso
Jul 21 2017 08:21
nice
@tetron I'm understanding there's an api also for workflow execution, right?
Peter Amstutz
@tetron
Jul 21 2017 08:22
yes
Paolo Di Tommaso
@pditommaso
Jul 21 2017 08:23
is any documentation available?
Paolo Di Tommaso
@pditommaso
Jul 21 2017 08:24
cool, thanks
Peter Amstutz
@tetron
Jul 21 2017 08:27
@pditommaso https://github.com/common-workflow-language/workflow-service is my reference implementation of WES
Thomas Cokelaer
@cokelaer
Jul 21 2017 08:38
For those interested in Snakemake, we can present Sequanix a graphical interface for snakemake workflows. We can organise an informal demo this afternoon that can also be used to discuss about Snakemake in general. Currently, we are hosting Sequanix under the Sequana project https://github.com/sequana/sequana
Brad Chapman
@chapmanb
Jul 21 2017 08:40
Awesome, if you want to pick a time and stick it on the Google Doc we can announce at lunch: https://docs.google.com/document/d/1PHN1qAWq1a2zM91oPYBy0DP2KKq5MbT6mdEQpH_kjbQ/edit#heading=h.ovzvso4bgv4d
Thomas Cokelaer
@cokelaer
Jul 21 2017 08:49
okay done, so this will happen at 2.30pm ; we'll see for a dedicated room/place later
Dennis Schwartz
@DennisSchwartz
Jul 21 2017 08:51
Is the intro to singularity still happening at 11?
Brad Chapman
@chapmanb
Jul 21 2017 08:56
Yes, happening now downstairs if you follow Paolo.
Hervé Ménager
@hmenager
Jul 21 2017 09:01
Farah Zaib Khan
@FarahZKhan
Jul 21 2017 09:14
@tetron Thanks Peter
rowlandm
@rowlandm
Jul 21 2017 09:20
Sorry @pditommaso - I won't be able to make it.
To your singularity talk
:(
Farah Zaib Khan
@FarahZKhan
Jul 21 2017 10:21
thanks for sharing @agbiotec :)
agbiotec
@agbiotec
Jul 21 2017 10:25
You are welcome !
Brad Chapman
@chapmanb
Jul 21 2017 10:27
Thanks Ntino -- added to the wiki.
Brad Chapman
@chapmanb
Jul 21 2017 10:33
Doing pre-lunch discussion in 5 minutes for anyone who wants to join. Hangout URL is: https://hangouts.google.com/call/46cq2fdgbvhmjds4nybn4tipiay
Michael L Heuer
@heuermh
Jul 21 2017 11:01
FYI, we landed a pull request for R support this morning, so we now have Python and R support (in addition to Scala and Java) for doing genomics at scale on Spark. If anyone is interested in taking the Python API for a test-drive, I should be able to help with setup and would appreciate any feedback.
rowlandm
@rowlandm
Jul 21 2017 11:24
That's pretty cool @heuermh
Paolo Di Tommaso
@pditommaso
Jul 21 2017 12:03
hackers, anybody has experience compiling protobuf java stubs?
Denis Yuen
@denis-yuen
Jul 21 2017 12:03
@pditommaso in the distant past, what are you running into?
Paolo Di Tommaso
@pditommaso
Jul 21 2017 12:04
dependencies :/
/Users/pditommaso/projects/nxf-tes-api/src/main/java/tes/TaskExecution.java:21513: error: package com.google.api does not exist
          com.google.api.AnnotationsProto.getDescriptor(),
                        ^
/Users/pditommaso/projects/nxf-tes-api/src/main/java/tes/TaskExecution.java:21631: error: package com.google.api does not exist
    registry.add(com.google.api.AnnotationsProto.http);
                               ^
/Users/pditommaso/projects/nxf-tes-api/src/main/java/tes/TaskExecution.java:21634: error: package com.google.api does not exist
    com.google.api.AnnotationsProto.getDescriptor();
                  ^
Denis Yuen
@denis-yuen
Jul 21 2017 12:04
@pditommaso sounds like a build system thing, is this with Maven?
Paolo Di Tommaso
@pditommaso
Jul 21 2017 12:05
I'm importing com.google.protobuf:protobuf-java:3.3.1 but it's not enough
gradle, bit it's not clear what libs I need to include
Michael L Heuer
@heuermh
Jul 21 2017 12:05
@pditommaso If it might work for you, I prefer the wire library from Square https://github.com/square/wire. It generates code with a nicer API.
Paolo Di Tommaso
@pditommaso
Jul 21 2017 12:06
does it consume protobug protobuf interface ?
Michael L Heuer
@heuermh
Jul 21 2017 12:06
Martin Cech
@martenson
Jul 21 2017 12:09
Could somebody please gather what is left of the galaxy/bioconda/biocontainers stickers around brmlab in the end of the day and bring it to BOSC? You can give it to me, @jmchilton, Bjoern Gruning, Berenice Batut or any other Galaxy person you see.
Thanks in advance if there is a good soul that does this for me. :100:
Thomas Cokelaer
@cokelaer
Jul 21 2017 12:29
we'll start the snakemake/sequanix discussion in a minute
asetGem
@asetGem
Jul 21 2017 12:30
in the basement!
Matúš Kalaš
@matuskalas
Jul 21 2017 12:38
Hey all, 3 pieces of useful information follow:
  • We are allowed to publish all photos from Brmlab. So please go ahead and share!
  • We'll have a group beer (with pub food) at Zly Casy near the congress centre tonight, from say 19.30 (to be confirmed). They advertise 48 taps with Czech premium smallbrew
  • The WiFi problems downstairs are due to switching between the upstairs and the downstairs network. So the only options are Ethernet or hiding away from the upstairs network.
Brad Chapman
@chapmanb
Jul 21 2017 12:44
Martin -- I'll grab the stickers. Matus -- awesome, Zly Casy looks perfect.
Paolo Di Tommaso
@pditommaso
Jul 21 2017 12:47
OK, I've managed to compile the GA4GH Task Execution java client
anybody has experience with this API ?
Peter Amstutz
@tetron
Jul 21 2017 12:48
@pditommaso Brian O'Connor is outside, you should talk to him
Paolo Di Tommaso
@pditommaso
Jul 21 2017 12:49
ah nice, he is joining the conference tomorrow, right?
Peter Amstutz
@tetron
Jul 21 2017 12:49
yes
Paolo Di Tommaso
@pditommaso
Jul 21 2017 12:50
:ok_hand:
Matúš Kalaš
@matuskalas
Jul 21 2017 12:52
Zly Casy (http://www.zlycasy.eu/) is booked for 7.30pm!
Sokratis Kariotis
@BioSok
Jul 21 2017 12:56
Cool
agbiotec
@agbiotec
Jul 21 2017 12:58
@matuskalas no beer garden :-(
but looks cool, I am in !
Matúš Kalaš
@matuskalas
Jul 21 2017 13:00
True. But it's in basements, so hopefully not way too hot. Still, a garden drink or food before or after is recommended ;-)
agbiotec
@agbiotec
Jul 21 2017 13:00
@matuskalas I am in in whatever you guys decide....
@BioSok are you at the Brmlab or remote ? Catch up during dinner to speak some Greek ? (my real name Konstantinos Krampis)
Sokratis Kariotis
@BioSok
Jul 21 2017 13:18
I am in second desk from the door :D
Matúš Kalaš
@matuskalas
Jul 21 2017 13:19
Brad Chapman
@chapmanb
Jul 21 2017 14:15
Peter Amstutz
@tetron
Jul 21 2017 14:35
@FarahZKhan @stain kwargs["make_fs_access"]
fsaccess = kwargs["make_fs_access"]("")
Maya Nedeljkovich
@mayacoda
Jul 21 2017 14:38
We have our first official binary release of the rabix composer up on github: https://github.com/rabix/composer/releases/tag/v1.0.0-beta.3
For everyone that was having a hard time getting it built (like me, all day today)
Brad Chapman
@chapmanb
Jul 21 2017 14:46
Nice one, so many people have asked for this. I'm excited to be able to point them at it.
Brad Chapman
@chapmanb
Jul 21 2017 15:02
Going to do Codefest wrap up in ~15 minutes. If anyone wants to joint remotely please ping us here so we can make sure you can hear and contribute.
Hervé Ménager
@hmenager
Jul 21 2017 15:06
thank you @njall
Paolo Di Tommaso
@pditommaso
Jul 21 2017 15:07
nice, we've managed to submit first jobs to funnel server via TES API, thanks @tetron and @briandoconnor !
tho are crashing :stuck_out_tongue_winking_eye:
Phil Ewels
@ewels
Jul 21 2017 15:08
we are too! Too hot :flushed:
Hervé Ménager
@hmenager
Jul 21 2017 15:10
:+1: @ewels - i suspect it could be a conspiracy to increase our beer consumption... that's my excuse, at least :stuck_out_tongue_winking_eye:
Phil Ewels
@ewels
Jul 21 2017 15:11
I'm happy to go along with that conspiracy :beers:
Matúš Kalaš
@matuskalas
Jul 21 2017 15:11
Wait for the Zly Casy, that will be a massacre ;-) :beers: :beers: :beers: :beers:
Martin Cech
@martenson
Jul 21 2017 15:26
'zly casy' == 'bad times' :D
Thanks @chapmanb !
agbiotec
@agbiotec
Jul 21 2017 15:52
https://hackmd.io/s/rJ9kzoyL- Kurbernetes on Google cloud documentation
Stian Soiland-Reyes
@stain
Jul 21 2017 16:16
Brad Chapman
@chapmanb
Jul 21 2017 16:49
Lost and found: I have one mac power supply with a US plug. I have it in my bag and will bring to BOSC tomorrow so let me know if it's yours.
Michael L Heuer
@heuermh
Jul 21 2017 17:00
@chapmanb That's mine, we're walking back to brmlab now, if yer still around
We're having trouble with the sec guard
Peter Amstutz
@tetron
Jul 21 2017 17:47
At Zly Casy with @chapmanb & others
Anyone else heading over?
Michael L Heuer
@heuermh
Jul 21 2017 17:55
We eventually got back in brmlab to retrieve our water bottle, crisis averted! I'll be heading to Zly Casy after I finish my slide, or if the party moves elsewhere before I get there, please let me know
Sokratis Kariotis
@BioSok
Jul 21 2017 19:00
Coming!