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  • Jan 31 2019 22:52
    matq007 commented #261
  • Jan 31 2019 22:49
    matq007 edited #261
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    matq007 opened #261
  • Jan 31 2019 14:33
    ewels edited #252
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  • Jan 31 2019 11:53
    apeltzer commented #252
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    pachiras commented #252
  • Jan 29 2019 20:42
    af8 starred nf-core/tools
  • Jan 29 2019 08:47

    nf-core-bot on api-doc

    Travis build: 816 (compare)

  • Jan 29 2019 08:42

    apeltzer on dev

    Markdown parsing: Fix all the e… Add new markdown rules to templ… Apparently whitespace isn't eno… and 2 more (compare)

  • Jan 29 2019 08:42
    apeltzer closed #260
  • Jan 28 2019 23:42
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    ewels review_requested #260
  • Jan 28 2019 22:57
    ewels review_requested #260
Phil Ewels
@ewels
What's nextflow -dockerize? I've never seen that option before
I'm not sure if setting -w ~/repo is a great idea either. Not sure what that will do. Any reason why you can't leave that as the default? (will end up being ~/repo/work/) 
  -d, -dockerize
     Launch nextflow via Docker (experimental)
Cool - so this puts nextflow itself inside docker? Any reason why this is useful?
Evan Floden
@evanfloden
I think quite a few people use it. Some people want to put Nextflow itself in a conainer to be ultra reproducible.
Phil Ewels
@ewels
ah ok, so that the underlying OS for the nextflow runtime is standardised?
I've never really thought about that before
Hugues Fontenelle
@huguesfontenelle
I'm not sure about -d nor -w, these were suggestions from Paolo
The -d he suggested after I tried Docker in Docker, where the bind path were wrong, https://groups.google.com/forum/#!topic/nextflow/bL9lZpvRFPE
I don't understand it too much, since you still need to install nextflow to be able to run nextflow -dockerize
Hugues Fontenelle
@huguesfontenelle

OK I got it:

It's not possible to use volume mounting with the docker executor, but using the machine executor it's possible to mount local directories to your running Docker containers. You can learn more about the machine executor here on our docs page.
ref

and Machine has become a pay feature
Hugues Fontenelle
@huguesfontenelle
(the default machine: true works though)
Phil Ewels
@ewels
nice!
marchoeppner
@marchoeppner
hi! got a question about the deepvariant pipeline. The documentation is missing information on where exactly the reference genomes come from - does anyone know, or do I have to start digging? ;)
marchoeppner
@marchoeppner
ah never mind, it's an S3 bucket...
Alexander Peltzer
@apeltzer
iGenomes Probably
Phil Ewels
@ewels
https://ewels.github.io/AWS-iGenomes/
arontommi
@arontommi
singularity image for deep variant is not on singularity hub
Alexander Peltzer
@apeltzer
Yeah saw it
just download from docker hub instead
singularity pull --name nf-core-deepvariant.simg docker://nfcore/deepvariant
I guess this singularity hub thing needs to either be solved soon or we need to get rid of the entire singularity documentation on our side as well
Current situation is confusing
arontommi
@arontommi

Thanks for addressing,
the "problem" with building it, is that it takes cpu, so locally is not always a possibility. and if you are working on "GDPR proof " cluster you dont have that option.

of course it is easy to get around this by having an open cluster somewhere, but that means another layer for someone to set up.

Phil Ewels
@ewels
yes exactly
using singularity hub has been very problematic though, so not an easy solution as we originally thought
but yes, leaving it half-hanging as a solution is not ideal
@apeltzer - did we ever try building on travis? I guess it takes too long?
Could be a good thing for Travis / GitHub actions etc to automatically build the docker image, convert to singularity and then push to singularity hub perhaps.
As I think it's just the automatic builds on singularity hub which won't work.
Sven F.
@sven1103
the shub api does not allow to push from remote i think
we had that discussion before if i remember correctly
Phil Ewels
@ewels
ah damn
Sven F.
@sven1103
that was the issue
so i voted for an own registry
Phil Ewels
@ewels
ah right, and then I said no we don't want our own hardware involved probably
Sven F.
@sven1103
or we get rid of singularity container registry support
yes, I remember you said sth like that
which I agree in principle
Phil Ewels
@ewels
I'm starting to wonder if we are going to need to set up some hardware at some point to keep scaling - singularity images and larger test sets
Sven F.
@sven1103
Lets put this on out phone call agenda next week
:)
can discuss some ideas
Phil Ewels
@ewels
:+1:
Sven F.
@sven1103
hardware and storage should not be an issue here
Phil Ewels
@ewels
hah, famous last words...
Sven F.
@sven1103
:D
I am more cautious of maintenance effort for self-hosted systems
thats what bothers me more