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    Michael Barton
    @michaelbarton
    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
    Michael Barton
    @michaelbarton
    https://circleci.com/gh/bioboxes/validator-short-read-assembler/111
    pbelmann
    @pbelmann
    nice
    so it was the cache?
    Michael Barton
    @michaelbarton
    The problem is here - https://github.com/bioboxes/velvet/blob/master/Dockerfile#L24