Add a Dockerfile

[ljdursi]

I'm having to make a docker image for an SGA somatic-variant-filter pipeline, so as part of that have made an SGA docker file; feel free to incorporate this into the sga repository if useful.

Note that in this docker image I have not included pysam or ruffus - or even python; this is just for running the SGA executable. We could also put together a dockerized version of the entire SGA workflow, but that would likely have a different interface; maybe something like that could go in sga-extra?

[jts]

Cool. I think that its fine to not include ruffus/pysam as that workflow is a bit dated. I could see there being demand for running preqc through docker so it might be worth including python/matplotlib at some point.

[ljdursi]

Good point, I'll do that right now and test it with what's in examples

[ljdursi]

Ok, done, with explanation in dockerfile comments. I note that make install doesn't put sga-preqc-report.py in ${prefix}/bin, is that intentional?

[jts]

No, that's an omission

[jts]

Thanks for the update, will merge

[mr-c]

FYI: Once Ubuntu syncs the Debian package of SGA to Ubuntu Xenial, one could request a backport to your favorite Ubuntu release.

Then you can skip compiling SGA and instead apt-get install sga it.

[jts]

Good to know, thanks.