add recent medaka versions

[kapsakcj]

Need testing and potentially fixing before merging into master & building on dockerhub.

These 3 images built successfully, but need to run data through.

I'm testing the 1.4.3 version and keep getting an error, but this may be due to malformed input data...not sure.

So this is a draft PR for now.

cc @matt-plumb

[erinyoung]

Sorry for taking so long to look at this. I'm going to build the 1.3.3 and 1.4.4 and test those. It looks like there's now a 1.5.

How often does medaka update?

[kapsakcj]

Thanks for taking a look, Erin. Currently have this as a "draft" PR since it's not ready for prime time. It's been a while since I tested these docker images, but remember hitting an error with at least one of them when running medaka consensus. I would really appreciate testing if you have some nanopore data handy

Medaka updates every 3-4 months-ish (https://github.com/nanoporetech/medaka/releases). They are up to 1.5.0 as of today, which is missing from this PR.

[erinyoung]

I tried to test these out, but I can't build the image locally in my setup unfortunately.

I pruned all my containers with

docker container prune

Removed everything in /var/lib/docker and /var/cache/apt/archives

And followed with

docker build --tag medaka_test:1.4.4 medaka_1.4.4

And it builds fine, but I run out of space.

Error processing tar file(exit status 1): write /medaka/venv/lib/python3.6/site-packages/medaka-1.4.4-py3.6-linux-x86_64.egg/exes/bgzip: no space left on device

And a similar error with 1.3.3

Error processing tar file(exit status 1): open /medaka/venv/lib/python3.6/site-packages/networkx/algorithms/connectivity/tests/__pycache__/test_edge_kcomponents.cpython-36.pyc: no space left on device

Installing also gave me the following error, but I don't know if this is important

Step 13/16 : RUN git lfs install
 ---> Running in bab86a1cd997
Error: Failed to call git rev-parse --git-dir --show-toplevel: "fatal: not a git repository (or any of the parent directories): .git\n"
Git LFS initialized.

I'll look into increasing the amount of space allocated to these relevant directories, but I thought I would let you know that I tried.

[kapsakcj]

Closing since I don't plan on revisiting this PR. ONT makes their own docker images available on dockerhub: https://hub.docker.com/r/ontresearch/medaka/tags

& dockerfile here: https://github.com/nanoporetech/medaka/blob/master/Dockerfile