Updates needed for rebuilding docker image

[jmtcsngr]

We needed to rebuild the docker image to run some containers and found a few changes were needed.

Github deprecated anonymous cloning using [email protected]:user/project.git urls. So replaced it with the https equivalent for the submodule.

The python:3.6 base image is not supported anymore because the base operating system is EOL. So replaced it with python:3.7 which I hope will not mean any big changes in behaviour python-wise. The switch of base image comes with an upgraded gcc which makes bwa building unhappy. So I used an explicit option for gcc during make. That is a known issue with bwa and stole the solution from bwa github issues. Also with the switch to python I had to upgrade versions of some of your python dependencies. I tried to upgrade things just enough to keep things compatible.

Also added some cleaning for apt to try to reduce the resulting image. That should have no impact in functionality but help to produce a slightly smaller image. And a pip update which is usually good to have.

We used the resulting image a couple of times and seems things are happy. But probably checking with some edge cases would be a good idea.

My neighbours here at Sanger are suggesting upgrading to a more recent samtools. But that will likely produce some small variations in output. So probably best to have a release with as few changes as possible and then make a release which may have breaking changes.