Add (incomplete) singularity interface #1805
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I said back in #1768 that I'd PR toil-vg's singularity module into Toil, so here it is. It seems to run okay for our purposes of calling command line tools in containers, except that the cache used to run Docker images on the fly gets easily overwhelmed. This is worked around by converting the images a priori (we could probably automate this if necessary). If Singularity ever made the cache size tunable, that'd probably work too.
There's still a lot of work to make this a drop-in replacement for docker.py:
I think would also require some thought for an abstract container interface. In toil-vg we wrap everything (https://github.com/vgteam/toil-vg/blob/master/src/toil_vg/vg_common.py#L87-L244) so it's easy to flip between docker/singularity/no-container. I think something similar is needed in Toil to make this useful. On a related note, singularity.py shares about 99% of its code with docker.py, so there may be room to refactor that a bit better too.