These are chat archives for chapmanb/obf-codefest

6th
Jul 2016
Spencer Bliven
@sbliven
Jul 06 2016 01:35
@chapmanb I'm also staying at the Hampton. I'll see you in the lobby tomorrow morning!
Chris Fields
@cjfields
Jul 06 2016 02:23
Staying at the Hawthorne Suites myself, will head to lobby tomorrow at 8:30 (will check back here though).
Paolo Di Tommaso
@pditommaso
Jul 06 2016 03:24
Hi there, I'm at Days Inn
Brad Chapman
@chapmanb
Jul 06 2016 04:25
Lorena and I made it safely to the Hampton Inn. See everyone here in the morning and we'll organize Ubers over to FamiLAB.
Hervé Ménager
@hmenager
Jul 06 2016 08:02
hello everyone,
Hervé Ménager
@hmenager
Jul 06 2016 08:08
not sure i can make it to the remote participation. but in the interest of everyone, are there any instructions for remote connection?
hangout, zoom, etc?
Phil Ewels
@ewels
Jul 06 2016 09:16
I guess everyone is asleep :sleeping: Time difference is going to be tough for us europeans! ;)
Heather L. Wiencko
@HLWiencko
Jul 06 2016 09:16
Some of us are awake ;)
But for me it’s just because I have to do work before gallivanting off and doing a hackathon
Phil Ewels
@ewels
Jul 06 2016 09:17
Wow! Isn't it 4-something in the morning? http://everytimezone.com/
Heather L. Wiencko
@HLWiencko
Jul 06 2016 09:17
It’s an entirely reasonable 5:17
I always end up doing this when I travel to the US, for some reason. It makes me a very dull person in the evenings, I think
Phil Ewels
@ewels
Jul 06 2016 09:19
Eases the jet lag I guess? Still, rather you than me.. :relaxed:
Heather L. Wiencko
@HLWiencko
Jul 06 2016 09:20
I’d have thought it made the jet lag better, but I still have trouble going back. The time change works in my favour coming this direction though, it’s a lot easier getting up early than it is at home
in any case, good morning. :)
Phil Ewels
@ewels
Jul 06 2016 09:20
Points for being the first I guess :)
Do you know what time things are starting?
Heather L. Wiencko
@HLWiencko
Jul 06 2016 09:20
I think things kick off at 9 local time
But there will be a lot of mooching and fooching around for the first hour or so, coffee and introductions and stuff like that.
What are you planning on working on?
Phil Ewels
@ewels
Jul 06 2016 09:24
There was some talk of working on new modules / features for MultiQC so I thought I could help out with that (I'm the author)
and you?
Heather L. Wiencko
@HLWiencko
Jul 06 2016 09:25
I’m not 100% sure. I thought I’d take a look at what’s needed in biopython at the moment, but I haven’t had a chance to sit down with it yet.
Is there a to-do list for MultiQC, or do people have modules in mind already?
Phil Ewels
@ewels
Jul 06 2016 09:28
I think @lpantano wanted to add some new modules that would be used for bcbio

This is what she wrote in the planning doc:

The idea of this project is to add any tools that are not already there, or improve the current ones.

Heather L. Wiencko
@HLWiencko
Jul 06 2016 09:30
cool. :)
Phil Ewels
@ewels
Jul 06 2016 09:44
This is the current to-do list of modules that have been requested if you're interested: https://github.com/ewels/MultiQC/milestone/6
HLWiencko @HLWiencko takes a look
Phil Ewels
@ewels
Jul 06 2016 09:51
Feel free to add a new issue if there are any others you'd like to see supported. Full list of existing ones on the github readme and http://multiqc.info/
Heather L. Wiencko
@HLWiencko
Jul 06 2016 09:57
Cool, I’ll have a think about it. Most of what I do in work is essentially collating results anyway, so there might be something I can add
Brad Chapman
@chapmanb
Jul 06 2016 10:44
@ewels and @hmenager, we're starting at 9am ET and will have a Hangout open. Thanks so much for joining remotely. I'll ping here when we're online at FamiLAB: https://hangouts.google.com/call/u5hvj2atabchvegkzeylsu5seme
Hervé Ménager
@hmenager
Jul 06 2016 11:26
Thank you @chapmanb. I'll do my best to join ;)
Christian Brueffer
@cbrueffer
Jul 06 2016 11:39
Anyone else at the Days Inn for ride-sharing to FamiLab?
Christian Brueffer
@cbrueffer
Jul 06 2016 11:47
Just saw you're here as well @pditommaso
Paolo Di Tommaso
@pditommaso
Jul 06 2016 11:53
@cbrueffer great s
@cbrueffer oops.. Great, do we meet at the reception at 8.30?
Christian Brueffer
@cbrueffer
Jul 06 2016 11:57
@pditommaso sounds good
Robin Andeer
@robinandeer
Jul 06 2016 12:31
We're leaving from Hawthorne soon :)
Michael R. Crusoe
@mr-c
Jul 06 2016 12:31
Last call for shared rise from the Hawthorne Suites!
Michael L Heuer
@heuermh
Jul 06 2016 13:10
Does anyone still need to get to Familab?
Paolo Di Tommaso
@pditommaso
Jul 06 2016 13:11
I guess Fabien Campagne
@heuermh btw who are you? :)
Michael L Heuer
@heuermh
Jul 06 2016 13:12
black t-shirt & beard!
Heather L. Wiencko
@HLWiencko
Jul 06 2016 13:31
There are two people here with black t-shirts and beards…you’re at a hackathon ;)
three if you count the person who’s actually wearing navy, but it’s hard to tell!
Paolo Di Tommaso
@pditommaso
Jul 06 2016 13:31
:)
Hervé Ménager
@hmenager
Jul 06 2016 13:31
@HLWiencko @heuermh is longer beard
;)
Heather L. Wiencko
@HLWiencko
Jul 06 2016 13:32
I did eventually figure it out, I just thought it was a funny choice of descriptions
Heather L. Wiencko
@HLWiencko
Jul 06 2016 13:44
can the remote guys hear us okay?
Phil Ewels
@ewels
Jul 06 2016 13:44
the last few people not so much
the current guy yes
Heather L. Wiencko
@HLWiencko
Jul 06 2016 13:44
Ok, it should get better from here, the last couple of us weren’t really facing the remote machine
Hervé Ménager
@hmenager
Jul 06 2016 13:45
not always, depends on the location
Michael L Heuer
@heuermh
Jul 06 2016 13:49
Topic list so far: Common Workflow Language (CWL)/Arvados, Nextflow, ADAM/Spark, MultiQC, Visualization/Structures
Heather L. Wiencko
@HLWiencko
Jul 06 2016 13:49
“workflows” is definitely the word of the day
Chris Fields
@cjfields
Jul 06 2016 13:51
definitely
Michael L Heuer
@heuermh
Jul 06 2016 13:54
Oh and BioPerl :)
Chris Fields
@cjfields
Jul 06 2016 13:54
Heh
Heather L. Wiencko
@HLWiencko
Jul 06 2016 13:54
there was a lot less biopython than I expected!
and way more bioperl ;)
John Fonner
@johnfonner
Jul 06 2016 13:54
What was that last project? Too quiet to hear
Chris Fields
@cjfields
Jul 06 2016 13:55
NextFlowWorkbench-y stuff
Heather L. Wiencko
@HLWiencko
Jul 06 2016 13:55
Language Workbench technology?
John Fonner
@johnfonner
Jul 06 2016 13:55
thanks
Chris Fields
@cjfields
Jul 06 2016 13:55
re: biopython, I know, was thinking Peter C was going to participate remotely
Lorena Pantano
@lpantano
Jul 06 2016 13:56
@ewels, do you have a list of things we can do in general for multiqc?
Christian Brueffer
@cbrueffer
Jul 06 2016 13:56
@HLWiencko Peter's not here, so I guess I'm in the minority ;-)
Phil Ewels
@ewels
Jul 06 2016 13:56
@lpantano: Absolutely! Modules here: https://github.com/ewels/MultiQC/milestone/6
Lorena Pantano
@lpantano
Jul 06 2016 13:56
nice!
Phil Ewels
@ewels
Jul 06 2016 13:56
That's the list of people that have requested already
So would be good to add to it too if people have anything else that they want
There are some others too - eg. smaller changes to your samtools module: ewels/MultiQC#251
Heather L. Wiencko
@HLWiencko
Jul 06 2016 13:58
so one of the reasons I was incuriated is because of what Brad mentioned — it might be easy enough to just put something together quickly for y’all
Phil Ewels
@ewels
Jul 06 2016 13:59
Absolutely - stuff like adding new submodules for Picard and samtools should be pretty quick to pick up
Just a case of using an existing submodule as a template and adjusting it to understand a similar but different kind of output
Heather L. Wiencko
@HLWiencko
Jul 06 2016 14:00
Is there sample data for either of those that I can start with?
In data/modules/samtools or picard
Heather L. Wiencko
@HLWiencko
Jul 06 2016 14:01
nice
Lorena Pantano
@lpantano
Jul 06 2016 14:01
Heather, do you want to come here with us?
Phil Ewels
@ewels
Jul 06 2016 14:01
For samtools idxstats and flagstat anyway
Lorena Pantano
@lpantano
Jul 06 2016 14:01
yellow t-shirt guy
Heather L. Wiencko
@HLWiencko
Jul 06 2016 14:02
I should probably make the trek over, one sec
Phil Ewels
@ewels
Jul 06 2016 14:02
hah, sorry for giving you a new nickname @robinandeer ;)
Should we move to https://gitter.im/ewels/MultiQC to stop spamming everyone else?
Lorena Pantano
@lpantano
Jul 06 2016 14:02
sure
Robin Andeer
@robinandeer
Jul 06 2016 14:06
@ewels it's fine ;)
So if people want to pool photos together I've set up a shared album
https://goo.gl/photos/QejrQQcsiCugzFPPA
Please let me know if it's complicated to get the uploading to work :)
Brad Chapman
@chapmanb
Jul 06 2016 14:16
If you haven't already, pleaes fill out Doodle poll for rides tomorrow: http://doodle.com/poll/ck76g2z6spd475wv
Michael L Heuer
@heuermh
Jul 06 2016 14:19
Yesterday I reconnoitered a few options for dinner, the one most likely to be able to handle a large group is Korea House http://www.koreahouseorlando.com/.
We'll put this up for discussion (along with other options) after lunch.
Christian Brueffer
@cbrueffer
Jul 06 2016 14:29
@HLWiencko just heard you want to look into Biopython, let me know if I can help
Heather L. Wiencko
@HLWiencko
Jul 06 2016 14:30
I think I’m going to try and put something together quickly for MultiQC — I want to get involved with Biopython at some stage, but it might be something I should look into over a longer timeframe
Dave Casey aka Da3v
@DaveCasey
Jul 06 2016 14:54
Once you have filled it out, find me, and I'll give you a badge. (I'm currently wearing a black "Warning I do my own science" shirt).
Heather L. Wiencko
@HLWiencko
Jul 06 2016 14:58
ha, I was just talking to you and didn’t think to ask
come back ;)
Michael R. Crusoe
@mr-c
Jul 06 2016 15:12
(the link above is a template for a CWL Diff design document)
@johnfonner Will you join us for lunch?
Phil Ewels
@ewels
Jul 06 2016 15:22
STAR function that makes a barplot: star_alignment_chart
John Fonner
@johnfonner
Jul 06 2016 15:25
@mr-c Yeah, I just need to find a way up there. It looks like Uber is ~$35. I'm over here at the Swan.
I could also just wait until tomorrow. I have a conference call with Bjorn Gruning at 1pm to talk about the cool stuff he's doing with automated Docker containers.
chengxi001
@chengxi001
Jul 06 2016 15:28
Thanks for clarify Mike! Everyone is invited to comment on the google doc https://docs.google.com/document/d/1-4PM4PLZxGphnG_mo-2KJp5Jx0GV_Rh1d5Rkdh7UpOc/edit?usp=sharing. Thanks
Robin Andeer
@robinandeer
Jul 06 2016 18:23
is there a hashtag for codefest/BOSC - is it the same for both events?
Heather L. Wiencko
@HLWiencko
Jul 06 2016 18:23
I think people are using #BOSC2016 for BOSC
There doesn’t seem to be a hashtag for Codefest
Brad Chapman
@chapmanb
Jul 06 2016 18:29
Using #BOSC2016 would be great
Heather L. Wiencko
@HLWiencko
Jul 06 2016 18:30
I like wrapping it in with #BOSC2016, that way other BOSC attendees can find out what we’re up to
Robin Andeer
@robinandeer
Jul 06 2016 18:30
:thumbsup:
Michael L Heuer
@heuermh
Jul 06 2016 18:32
The codefest has done it, we've broken github!
...and we're back!
Ben Busby
@DCGenomics
Jul 06 2016 19:25
For twitter I used #BOSC2016 #codefest
Ben Busby
@DCGenomics
Jul 06 2016 19:42
h/t Fabien Campagne
Robin Andeer
@robinandeer
Jul 06 2016 23:11
See you guys
Tomorrow - gonna try to rest up and get rid of my cold :)
Dave Casey aka Da3v
@DaveCasey
Jul 06 2016 23:17
A plaid backpack was left behind. I have it here at the restaurant.