search

datashield / docker-rock

Rock R server with DataSHIELD packages inside
0 stars 4 forks source link

Docker rock for survival package #2

Open tombisho opened 2 years ago

tombisho commented 2 years ago

Is this the repo I should use to create a Rock image for survival analysis?

ymarcon commented 2 years ago

See https://github.com/obiba/docker-rock-demo/tree/survival

tombisho commented 2 years ago

Thanks, I will certainly make use of that 😀

Maybe my question should have been, is this the correct home for a survival analysis image, rather than one that is in a "demo" repo?

ymarcon commented 2 years ago

dsSurvival package is not in the official Datashield's Github. You should build and publish your own image, using this example. If you do so, I'll use it in opal-demo.obiba.org in place of this demo one.

StuartWheater commented 2 years ago

I was wondering what is the plan if an docker image is needed which contains both dsMediation, dsExposome and dsSurvival? Do we need a Community Docker Hub account?

ymarcon commented 2 years ago

We can't do all combinations, then it is up to the consortium to make their own images. And they would probably use a private docker repo, just like Inesctec does with Coral for Recap.

tombisho commented 2 years ago

Yes although it might be nice for consortia to share to reduce work?

On Thu, 16 Jun 2022, 17:15 Yannick Marcon, @.***> wrote:

We can't do all combinations, then it is up to the consortium to make their own images. And they would probably use a private docker repo, just like Inesctec does with Coral for Recap.

— Reply to this email directly, view it on GitHub https://github.com/datashield/docker-rock/issues/2#issuecomment-1157859595, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACBAPNRFC4QNCVXJPLRJW3LVPNG57ANCNFSM5Y7EUNAQ . You are receiving this because you authored the thread.Message ID: @.***>

tombisho commented 2 years ago

And yes I can see that I should create my image in the Github where the package has been created...

ymarcon commented 2 years ago

You could have the Dockerfile within your R package source repo, for user reference. Just declare it in a .Rbuildignore file so that it does not get packaged.

tombisho commented 2 years ago

Yes that sounds like a good idea.

And then if I build an image, can it live in the DataSHIELD docker hub account (like for omics and exposome)? Or is this where we need some kind of audit?

On Thu, 16 Jun 2022, 19:55 Yannick Marcon, @.***> wrote:

You could have the Dockerfile within your R package source repo, for user reference. Just declare it in a .Rbuildignore file so that it does not get packaged.

— Reply to this email directly, view it on GitHub https://github.com/datashield/docker-rock/issues/2#issuecomment-1158024632, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACBAPNXEMKQDPLHUWVN7NV3VPN2B5ANCNFSM5Y7EUNAQ . You are receiving this because you authored the thread.Message ID: @.***>

ymarcon commented 2 years ago

omics and exposome should be in https://hub.docker.com/u/brgelab space. You should have your own as well.

tombisho commented 2 years ago

Ok great - I'll do that

On Fri, 17 Jun 2022, 10:54 Yannick Marcon, @.***> wrote:

omics and exposome should be in https://hub.docker.com/u/brgelab space. You should have your own as well.

— Reply to this email directly, view it on GitHub https://github.com/datashield/docker-rock/issues/2#issuecomment-1158707813, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACBAPNWBNPJY2NK4IHKYHA3VPRDKZANCNFSM5Y7EUNAQ . You are receiving this because you authored the thread.Message ID: @.***>

StuartWheater commented 7 months ago

dsSurvival is in new profile "dolomite-beach"