Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
    pbelmann
    @pbelmann
    @michaelbarton could you take a look at my PR with the developer guide?
    Paolo Di Tommaso
    @pditommaso
    Hi @michaelbarton
    I was wondering if the yaml input/output definition is going to be required in all kind of containers that will make part of the bioboxes specification
    Michael Barton
    @michaelbarton
    Yes with the current specification. It’s the best way we have come up with for transferring data between the user and container.
    Do you have an alternative suggestion?
    Paolo Di Tommaso
    @pditommaso
    that mean that one will have to create a yaml file in order to launch a container
    Michael Barton
    @michaelbarton
    Yes
    Paolo Di Tommaso
    @pditommaso
    it's that quite unhandy, don't you think that?
    Michael Barton
    @michaelbarton
    Yes I do
    However it is the only sane way to deal with complicated data we could think of.
    Paolo Di Tommaso
    @pditommaso
    the beauty of Docker is that you can interact quickly with containers with cmd line
    Michael Barton
    @michaelbarton
    We originally started with using environment variables passed to the container, but it quickly became complicated.
    Paolo Di Tommaso
    @pditommaso
    in fact, I was remembering that
    why don't you use command line parameters?
    Michael Barton
    @michaelbarton
    because if you are specifying multiple fasta files with different insert sizes it quickly becomes just as difficult.
    The issue is #61
    It was the longest discussion we had.
    I would be happy to read a proposal for a simpler interface, however I would ask that you read that discussion first.
    Paolo Di Tommaso
    @pditommaso
    ok, now that you pointed out the issue I will read that thanks
    Michael Barton
    @michaelbarton
    Thanks. We do welcome input from everyone. I know you have a lot experience from nextflow.io, so I would be glad to read any feedback or suggestions you have.
    Paolo Di Tommaso
    @pditommaso
    surely
    ah, I think there's a typo in at this page
    http://bioboxes.org/guide/developer/build-your-image/
    using the BASE directive
    should not be:
    using the FROM directive
    Michael Barton
    @michaelbarton
    Thanks for spotting that - bioboxes/bioboxes.org#35
    If you have any suggestions for the website, we welcome those too.
    A PR ekcetera ..., everything is up for discussion.
    I hope this standard will be developed by the community rather than only by me and @pbelmann.
    Paolo Di Tommaso
    @pditommaso
    it looks nice, I would make just larger and with a bigger font
    Michael Barton
    @michaelbarton
    The font is difficult to read?
    Paolo Di Tommaso
    @pditommaso
    not difficult, but there's a lot of empty space
    a bigger font would be more confortable
    Screen Shot 2015-04-28 at 23.34.59.png
    Michael Barton
    @michaelbarton
    If you refresh that page, it should say FROM now.
    Paolo Di Tommaso
    @pditommaso
    yep!
    btw, are you coming to Docker symposium at King's College, aren't you ?
    Michael Barton
    @michaelbarton
    I hope so. I have to work it out with the JGI so that I will be allowed to attend.
    Paolo Di Tommaso
    @pditommaso
    I see, hope to see you there if so
    Michael Barton
    @michaelbarton
    Yes, it would be good to meet you in person.
    I would like to meet everyone in the bioinformatics community who has been experimenting with Docker too.
    Michael Barton
    @michaelbarton
    This looks great @pbelmann. Thanks for fixing the problem.
    pbelmann
    @pbelmann
    Michael can we merge bioboxes/validator-short-read-assembler#27 ,so the validator works with the new file-validator?
    Michael Barton
    @michaelbarton
    I’ll start a rebuild on the CI server - https://circleci.com/gh/bioboxes/validator-short-read-assembler/110
    pbelmann
    @pbelmann
    great. Sorry for the merge conflicts.
    Michael Barton
    @michaelbarton
    No problem. That PR was very useful.
    It looks like there some lxc-start problems on circleci
    I’ll clear the cache and rebuild, I think the previous build of velvet with the old file validator is included.
    pbelmann
    @pbelmann
    ok