add recent versions of medaka

[kapsakcj]

Started a dockerfile on a separate branch, medaka-dev. https://github.com/StaPH-B/docker-builds/commit/641a2aeb089f86d063974d73f599b10530a87102

Docker image builds ok locally. Haven't run any data through to verify functionality.

Not ready to merge & build on dockerhub until I know it works

[kapsakcj]

I will add that it is quite large in size when uncompressed. here it is compared to the staphb/medaka:latest tag

$ docker images | grep medaka
kapsakcj/medaka                            1.3.3                           9964c8b858c6   8 minutes ago   4.08GB
staphb/medaka                              latest                          85e2812e69e0   5 months ago    3.96GB

[erinyoung]

There has to be a way to make the container smaller...

[kapsakcj]

the models are what makes them so large. I think there might be a way, at least with later versions of medaka, to install w/out the models and the user could download them on the fly with medaka tools download_models --models <model-name>

also I just realized that ONT is now providing a docker image for Medaka >=1.4.3. Listed on the README https://github.com/nanoporetech/medaka and is here on dhub https://hub.docker.com/r/ontresearch/medaka/tags

[erinyoung]

Thanks! I got their medaka container to work, and I'll be using that one until your pull request is more complete.

Their container is also very large and I had to change my TMPDIR variable in order to download it.

[erinyoung]

I'm closing this issue, because there's a duplicate one that's newer.

This issue can be re-opened if it would be helpful.