Updates needed for rebuilding docker image #10
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switch git for https address of repository
upgrade base image to python:3.7 to fix issue with debian EOL channels
picking from lh3/bwa#267
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We needed to rebuild the docker image to run some containers and found a few changes were needed.
Github deprecated anonymous cloning using
git@github.com:user/project.giturls. So replaced it with the https equivalent for the submodule.The
python:3.6base image is not supported anymore because the base operating system is EOL. So replaced it withpython:3.7which I hope will not mean any big changes in behaviour python-wise. The switch of base image comes with an upgradedgccwhich makesbwabuilding unhappy. So I used an explicit option forgccduringmake. That is a known issue withbwaand stole the solution frombwagithubissues. 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
aptto try to reduce the resulting image. That should have no impact in functionality but help to produce a slightly smaller image. And apipupdate 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.