Building docker images from Dockerfile no longer works easily. There are several reasons for this:
Possibly the biggest reason: installing older versions of software using biomanager in R is not easy (or at least unclear to me)! Many algorithms built in R are bound to fail eventually due to a lack of easy way to specify the version of the dependencies used. Moreover, many new builds can fail even if some nested dependencies of certain packages are no longer compatible (depending on how they are set-up internally). One year in, setting up Scribe from Dockerfile already doesn't work (see issue https://github.com/Murali-group/Beeline/issues/45) 🤷.
Some algorithms used in BEELINE come from github repos. If for some reason, the owner of those repos updates/removes a public repo (even if they are pointed to an older commit); the docker set-up is not going to work (!).
Any other system commands might pose a problem too (for example: the line RUN apt-get update in the Dockerfiles is needed to install some packages/libraries, and can potentially break things down the line).
The only way I can think of getting around this issue is to make the images built at the time of manuscript preparation available via Docker hub. While building an image using Dockerfile should work (until it wont), the initial set-up going forward is to going to pull an existing image instead of relying on Dockerfiles.
Here are the steps needed to push existing images (for future reference):
Login docker login --username <your username>
Find image ID for the pre-built docker image using docker images
Tag a local image: docker tag <image ID> <docker hub username>/<algorithm name>:<tag>
Alternative to steps 2-3 is to just append your docker hub username to existing images docker tag <algorithm name>:<tag> <docker hub username>/<algorithm name>:<tag>
Push to docker hub: docker push <docker hub username>/<algorithm name>:<tag>
If for some reason you need to update an existing image to create new versions:
Run the docker to make changes: docker run -it <docker hub username>/<algorithm name>:<tag> /bin/bash
Once inside the container, make your changes; exit the docker. Since we did not use --rm flag while running docker in the previous step, the modified container will be available for later use, even after exiting.
Access the modified container id by using docker ps -a
Building docker images from Dockerfile no longer works easily. There are several reasons for this:
RUN apt-get updatein the Dockerfiles is needed to install some packages/libraries, and can potentially break things down the line).The only way I can think of getting around this issue is to make the images built at the time of manuscript preparation available via Docker hub. While building an image using Dockerfile should work (until it wont), the initial set-up going forward is to going to pull an existing image instead of relying on Dockerfiles.
An example image is already available here: https://hub.docker.com/repository/docker/grnbeeline/scribe
Here are the steps needed to push existing images (for future reference):
docker login --username <your username>docker imagesdocker tag <image ID> <docker hub username>/<algorithm name>:<tag>docker tag <algorithm name>:<tag> <docker hub username>/<algorithm name>:<tag>docker push <docker hub username>/<algorithm name>:<tag>If for some reason you need to update an existing image to create new versions:
docker run -it <docker hub username>/<algorithm name>:<tag> /bin/bash--rmflag while running docker in the previous step, the modified container will be available for later use, even after exiting.docker ps -adocker commit <container ID> <docker hub username>/<algorithm name>:<new tag>docker push <docker hub username>/<algorithm name>:<new tag>