set HOME, TMPDIR, TEMP, TMP sensibly inside container

[o-smirnov]

The discussions in caracal-pipeline/caracal#1200 and ratt-ru/ragavi#78 highlight the fact that some packages are naughty, and like to open temp files in locations different to the nominal output directory -- which may be on a different filesystem even, thus causing strange IO errors such as "no space on device".

Stimela can be defensive about this: set HOME, TMPDIR, TEMP and TMP inside the container to the output directory, so that these problems are preempted.

[Mulan-94]

@o-smirnov, so I shouldn't change this in ragavi?

[gigjozsa]

This would be great but it is hard to do it consistently as some software is even naughtier and hardcodes e.g. $HOME as /home/$USER, and then it would be great to provide some variables to redirect those directories (consistently) elsewhere (if for some reason those places are not the desired ones, if you e.g. want to share them across users), and put a big warning somewhere. Currently, for example in caratekit the user can temporarily redefine $HOME or some singularity folders, and that would be affected by a redirecting policy.

[o-smirnov]

Well, naughty software will always be cleverer than us, and this suggestion isn't a silver bullet. But just because it's not 100% foolproof doesn't mean it's not worth doing. It's simple and it protects from some naughtiness. For example, it will make us play nice with all software that relies on Python's tempfile module.