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    Ryan Williams
    @ryan-williams
    ok we're going in a moment
    Tony Yang
    @tonyyzy
    @ryan-williams get closer to the land when you pass the secone bridge!
    and shout BOSC!
    Michael R. Crusoe
    @mr-c
    Dinner at 8:15PM Markthalle
    Steinentorberg 20, 4051 Basel, Switzerland
    https://maps.app.goo.gl/9o2FSeXq8wKA5T1p8
    Adelaide Rhodes
    @Arhodes-Broad
    We are in [Toby, Tony, me]
    Nomi Harris
    @nlharris
    I’ll be there, but I’ll be late (probably more like 8:45).
    By the way, the seating area that’s through a door just to the left of the Hausbar is air-conditioned!
    Yo Yehudi
    @yochannah
    I'm on my way but running late too! 😁
    jessMaia
    @jessMaia
    Same here, running late, just got on the tram
    Adelaide Rhodes
    @Arhodes-Broad
    I am sitting at Haus Bar
    Hilmar Lapp
    @hlapp
    Just when was able to leave for the tram the heavens open up. And there’s more forecast. See you all tomorrow!
    Kaushik Ghose
    @kaushik-work
    Well, the monsoons are here ...
    Matúš Kalaš
    @matuskalas
    Indeed! :D
    Peter Cock
    @peterjc
    I am in the venue already for Saturday morning (as the key holder), not sure when the exterior door switches to opening automatically. I have picked up more apples and bananas.
    Goals document (please add links to other docs and slides): https://docs.google.com/document/d/1UaScEaOchWPCTdBei8PLCIcKLEqVdhDimOj4zFydhnk/edit?usp=sharing
    Day one outputs slides (please update as needed): https://docs.google.com/presentation/d/1gwN5dK5FAN_5Hag2qkJNfsMYfWqgnSlrxNbqKyh1b4w/edit#slide=id.g5ee9ca272f_0_54
    Peter Cock
    @peterjc
    I will wait in the ground floor auditorium - tap the glass to get me to come and open then outside door if it doesn't open automatically (hoping that is on a timer from 9am, if not may have to ask hosts advice).
    Kaushik Ghose
    @kaushik-work
    Friends, I've made a wimpy decision to continue CoFest remotely from the airport. The projected rain did not help my decision. It was so great to see you all again (or meet you for the first time) in person! A big thank you to all the organizers! See you on the gitter and on the google doc shortly.
    Spencer Bliven
    @sbliven
    Does biopython have a gitter/slack channel?
    Michael L Heuer
    @heuermh
    Rough schedule for today:
    12:00 pm lunch
    5:00 pm wrap up, please have slides ready at https://docs.google.com/presentation/d/1h5COAKc4SLBYNkv9OLjLXAPSu9CPrSbpBBFOTxzpt2E/edit
    6:00 pm clean up space, wash dishes, take out trash, etc.
    W. Lee Pang, PhD
    @wleepang
    @peterjc - see: https://github.com/aws-samples/aws-genomics-workflows
    Peter Cock
    @peterjc
    @sbliven @chapmanb I don't think so, should we make one under OBF?
    @kaushik-work Thanks for coming and safe travel home - the rain last night was impressive, so far OK today.
    @wleepang Thank you for that example of using miniconda on TravisCI - it looks fairly simple. I've previously used conda on CircleCI via VM image with miniconda already installed - see https://github.com/peterjc/thapbi-pict/blob/master/.circleci/config.yml
    Michael L Heuer
    @heuermh
    I don't think so, should we make one under OBF?
    I'd recommend creating one associated with the github repo, then gitter shows repo activity, links issues, etc.
    W. Lee Pang, PhD
    @wleepang
    @peterjc - No prob! Thanks for the example on CircleCI!
    W. Lee Pang, PhD
    @wleepang
    biopython folks - is there a way to have the SeqIO parse a file-like handle in binary mode?
    W. Lee Pang, PhD
    @wleepang
    @peterjc - here's a public fastq file for testing:
    s3://1000genomes/phase3/data/NA12878/sequence_read/SRR622461.filt.fastq.gz
    Tony Yang
    @tonyyzy
    @mr-c https://www.biostars.org/p/366246/
    Peter Cock
    @peterjc
    @wleepang and I are trying to use Python's TextIOWrapper on top of the boto3 handle like object to get a (unicode) text mode handle for parsing, rather than the default binary handle (bytes).
    @heuermh How does that work? Making a gitter associated with a github repo?
    Mateusz Kuzak
    @mkuzak
    @peterjc in respect to your question in the morning, here is the schema to validate the cff file https://github.com/citation-file-format/schema
    Michael L Heuer
    @heuermh
    Honestly, I don't remember. But at some point I did it for https://gitter.im/biojava/biojava and https://gitter.im/bigdatagenomics/adam
    Michael R. Crusoe
    @mr-c
    @mkuzak :+1:
    Peter Cock
    @peterjc
    @wleepang has a small example working via https://pypi.org/project/smart-open/ which defaults to opening files in text mode (unicode), which is perfect. Large examples seem to work too. You do however need AWS S3 credentials setup, even for a public dataset.
    W. Lee Pang, PhD
    @wleepang
    @peterjc - example gist here:
    https://gist.github.com/wleepang/d17e0b18476d45860893313e2d78b3eb
    Michael L Heuer
    @heuermh
    @peterjc This is what I was referring to, https://github.com/biojava/biojava-adam
    I wonder if something similar might be useful for biopython, converting from seq records to DataFrame on Spark, Parquet on disk
    Michael L Heuer
    @heuermh
    Wrapping up now! Must . . . finish . . . slides . . .
    Stian Soiland-Reyes
    @stain
    Put in some belated update, I guess you finished now..?
    Peter Cock
    @peterjc
    About to leave when rain stops, then beer and dinner
    Mateusz Kuzak
    @mkuzak
    enjoy
    Yo Yehudi
    @yochannah
    So what was the name of the pub we're meeting at? @hlapp
    Hilmar Lapp
    @hlapp
    Kabar
    Kaserne Basel, Klybeckstr
    Michael R. Crusoe
    @mr-c
    @stain I'd still like seeing your updates!
    Hilmar Lapp
    @hlapp
    @yochannah Tram line 8, direction Neuweilerstr. Exit Kaserne.
    @yochannah Michael H and I are in the tram. It’s waiting, departs 6:29
    I don’t see you guys - you can’t be that far behind?
    Toby Hodges
    @tobyhodges
    on my way by foot
    there by 19:30