wrap cworld into a docker image/container/whatever

sergpolly commented 5 years ago

We need this real bad, since some people are still using cworld for some things, but maintenance and installation becomes problematic ... @betulakgol I really want to do it this week - i know you were interested - let's coordinate the time sometime this week

betulakgol commented 5 years ago

@sergpolly we can do it late afternoon tomorrow (after 3:30) or Friday afternoon.

sergpolly commented 5 years ago

@betulakgol let's do today after 3:30

sergpolly commented 5 years ago

started with distiler_env image: https://github.com/mirnylab/distiller-nf/tree/master/docker , just to try - by removing a bunch of stuff from the Dockerfile
docker build .
docker tag IMGID user/imagename
docker login
docker push user/imagename

trying it on the cluster

singularity pull docker://user/imagename (if fails use interactive)
singularity shell imagename.simg (shell in and browse around, mount /nl etc)

editing existing image, back on the PC:

docker run -dit IMGID (-dit is a trick to prevent "static" container from exiting immidiately)
docker ps -a (to check if it is running indeed)
docker exec -it CONTID bash (execute bash in a running container based on IMGID)
do stuff inside of the container, e.g. apt-get install something or mkdir /nl , exit when done
docker commit CONTID user/imagename (maybe with a -m message part - to know what changed)
docker push user/imagename

Now the Dockerhub image should be updated ...

TODO:

proceed with the actual cworld installation in a docker image: https://github.com/dekkerlab/cworld-dekker#installation
Most important thing to do is to fix conda installation of cworld dependencies using this: https://github.com/dekkerlab/cworld-dekker#conda-installation
it would require "manual" updates to the image, which could be commited and push to dockerhub just fine.
Make docker(the file,build and release scripts) a part of this repository itself
Update docs to announce end of maintenance and to recommend using cworld via container

sergpolly commented 5 years ago

relevant: https://www.techrepublic.com/article/how-to-commit-changes-to-a-docker-image/

dekkerlab / cworld-dekker