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    Pjotr Prins
    @pjotrp
    Amazon wants to sponsor pubseq data hosting btw
    Michael R. Crusoe
    @mr-c
    @pjotrp Great news!
    @pjotrp please share your scripts with @SasSwart
    Will be fun to try out the federation feature some day
    Pjotr Prins
    @pjotrp
    I think we'll get there
    https://github.com/arvados/bh20-seq-resource/blob/master/workflows/tools/pubseq-fetch-ids fetches IDs hosted on PubSeq
    and https://github.com/arvados/bh20-seq-resource/blob/master/workflows/tools/pubseq-fetch-data.py fetches all records based on those IDs
    You'll need Ruby 3 for the first script. Sorry :)
    I just could not resist using pattern matching.
    Pjotr Prins
    @pjotrp
    After rewriting the GenBank parser and normalization I am almost ready to submit a new batch of sequences so we should get at 50K sequences.
    After that we'll start looking at getting raw sequencing data done!
    Michael R. Crusoe
    @mr-c
    Hey @pjotrp , you broke the repo at https://github.com/arvados/bh20-seq-resource/commit/1c4e055b8a9dc53b7fdbdf12d4b0a7e877fbc2ef#diff-485e113b22be66a831ab15ae5909d5465fecd92cbec771939700132ad145afbd :cry:
    Pjotr Prins
    @pjotrp
    Darn, I did, didn't I :)
    I'll role it back. submodules and me don't agree ;)
    Must say that workflows/tools is a natural place to put stuff!
    Michael R. Crusoe
    @mr-c
    @pjotrp please send PRs to bio-cwl-tools ; thanks!
    Pjotr Prins
    @pjotrp
    That is for CWL only, right?
    Michael R. Crusoe
    @mr-c
    @pjotrp yes, that's the source of the workflow/tools git submodule
    Pjotr Prins
    @pjotrp
    I thought so, I need to move the scripts to a different dir
    Michael R. Crusoe
    @mr-c
    Can someone submit a PR to add PubSeq to https://github.com/CDCgov/SARS-CoV-2_Sequencing#bioinformatics ?
    Pjotr Prins
    @pjotrp
    Yeah, we should do that. I also need to fix that repo ;)

    A reminder that thanks to our organising team we have a great line up
    for FOSDEM:

    https://fosdem.org/2021/schedule/track/declarative_and_minimalistic_computing/

    with famous Guix contributors and Guixers doing the moderating :) All
    virtual and online this year, so you can attend from anywhere! Put
    Sunday February 7th in your diary!

    And then on Monday 8th we have another Guix day online as a low
    profile unconference. Do sign up and we'll send a reminder here. See

    https://libreplanet.org/wiki/Group:Guix/FOSDEM2021

    Pjotr Prins
    @pjotrp

    Hey @pjotrp , you broke the repo at https://github.com/arvados/bh20-seq-resource/commit/1c4e055b8a9dc53b7fdbdf12d4b0a7e877fbc2ef#diff-485e113b22be66a831ab15ae5909d5465fecd92cbec771939700132ad145afbd :cry:

    Should be fixed now

    1 reply
    Pjotr Prins
    @pjotrp
    One test sequence in preparation for the direct sequencer uploads is now on PubSeq
    Michael R. Crusoe
    @mr-c
    https://biohackathon.curii.com/ 's SSL certificate has expired
    @tetron How do we seed the SURFsara (NL) pubseq with the data + workflows from the AWS (USA) pubseq?
    Pjotr Prins
    @pjotrp
    I have a broader question: now we can host our data on AWS Open Data we have parties interested in using our workflow for data analysis. I need help though! Particularly where it comes to adapting CWL workflows. Who'd be interested in helping to actively develop the pipeline? Note that there may be grant money down the line - especially if we create something useful. @mr-c maybe we should do a brainstorming session in the coming days?
    Note that the US is going to pour money into sequencing COVID19. If we can keep up with Genbank etc. I think people will use PubSeq for analysis. Mostly because we do some automated curation, but also because we have some end-products (pangenome, VCF, phylo tree).
    Michael R. Crusoe
    @mr-c
    @pjotrp Sure, but my capacity beyond a meeting here and there is fully booked for the next 36-48 months
    in the short term I am eager to demonstrate parity between the NL and USA pubseqs
    Pjotr Prins
    @pjotrp
    Yeah, I know. I am in a bad place too when it comes to effort. That is why I am asking for help!
    Would a GSoC proposal be an idea?
    Michael R. Crusoe
    @mr-c
    they are half-as-long and for half-as-much-$$ this year
    Pjotr Prins
    @pjotrp
    I think Elixir wants to participate, but I can't get hold of the right people and the docs are read-only.
    Yeah, I know. Not too concerned about that.
    Michael R. Crusoe
    @mr-c
    I know people...
    Pjotr Prins
    @pjotrp
    180 hours and a motivated student would be great
    How about a chat around lunch tomorrow?
    I can draft a proposal beforehand
    Michael R. Crusoe
    @mr-c
    Sure: send me a calendar invite :-)
    Pjotr Prins
    @pjotrp
    Done. Anyone here interested in building out CWL workflows for COVID-19?
    Pjotr Prins
    @pjotrp
    maybe I should ask on the CWL channel/ML?
    Peter Amstutz
    @tetron
    Outreachy?
    Pjotr Prins
    @pjotrp
    GSoC
    Peter Amstutz
    @tetron
    @pjotrp I meant Outreachy is kind of like GSoC as a way to get potential interns
    Pjotr Prins
    @pjotrp
    yeah, but I understand it is less about programming skills
    Michael R. Crusoe
    @mr-c
    @pjotrp there are definitely programmers available via Outreachy
    Pjotr Prins
    @pjotrp
    I just moved the website to https. Some components are still http https://covid19.genenetwork.org/
    Pjotr Prins
    @pjotrp
    Would it be worth organising another biohackathon in March? Maybe small scale and focused on PubSeq this time? I have mixed feelings about the one last year, but it rendered dividends.
    Pjotr Prins
    @pjotrp
    PubSeq is now officially part of the AWS Open Data Sponsorship Program